diff --git a/common/thread_flags.aconfig b/common/thread_flags.aconfig
index 14b70d0..60120bc 100644
--- a/common/thread_flags.aconfig
+++ b/common/thread_flags.aconfig
@@ -35,3 +35,12 @@
     description: "Controls whether the Android Thread Ephemeral Key feature is enabled"
     bug: "348323500"
 }
+
+flag {
+    name: "set_nat64_configuration_enabled"
+    is_exported: true
+    is_fixed_read_only: true
+    namespace: "thread_network"
+    description: "Controls whether the setConfiguration API of NAT64 feature is enabled"
+    bug: "368456504"
+}
diff --git a/framework-t/api/system-current.txt b/framework-t/api/system-current.txt
index 09a3681..08129eb 100644
--- a/framework-t/api/system-current.txt
+++ b/framework-t/api/system-current.txt
@@ -506,6 +506,13 @@
     field @NonNull public static final android.os.Parcelable.Creator<android.net.thread.ThreadConfiguration> CREATOR;
   }
 
+  @FlaggedApi("com.android.net.thread.flags.set_nat64_configuration_enabled") public static final class ThreadConfiguration.Builder {
+    ctor @FlaggedApi("com.android.net.thread.flags.set_nat64_configuration_enabled") public ThreadConfiguration.Builder();
+    ctor @FlaggedApi("com.android.net.thread.flags.set_nat64_configuration_enabled") public ThreadConfiguration.Builder(@NonNull android.net.thread.ThreadConfiguration);
+    method @FlaggedApi("com.android.net.thread.flags.set_nat64_configuration_enabled") @NonNull public android.net.thread.ThreadConfiguration build();
+    method @FlaggedApi("com.android.net.thread.flags.set_nat64_configuration_enabled") @NonNull public android.net.thread.ThreadConfiguration.Builder setNat64Enabled(boolean);
+  }
+
   @FlaggedApi("com.android.net.thread.flags.thread_enabled") public final class ThreadNetworkController {
     method @FlaggedApi("com.android.net.thread.flags.epskc_enabled") @RequiresPermission("android.permission.THREAD_NETWORK_PRIVILEGED") public void activateEphemeralKeyMode(@NonNull java.time.Duration, @NonNull java.util.concurrent.Executor, @NonNull android.os.OutcomeReceiver<java.lang.Void,android.net.thread.ThreadNetworkException>);
     method public void createRandomizedDataset(@NonNull String, @NonNull java.util.concurrent.Executor, @NonNull android.os.OutcomeReceiver<android.net.thread.ActiveOperationalDataset,android.net.thread.ThreadNetworkException>);
@@ -520,6 +527,7 @@
     method @RequiresPermission(android.Manifest.permission.ACCESS_NETWORK_STATE) public void registerStateCallback(@NonNull java.util.concurrent.Executor, @NonNull android.net.thread.ThreadNetworkController.StateCallback);
     method @RequiresPermission("android.permission.THREAD_NETWORK_PRIVILEGED") public void scheduleMigration(@NonNull android.net.thread.PendingOperationalDataset, @NonNull java.util.concurrent.Executor, @NonNull android.os.OutcomeReceiver<java.lang.Void,android.net.thread.ThreadNetworkException>);
     method @FlaggedApi("com.android.net.thread.flags.channel_max_powers_enabled") @RequiresPermission("android.permission.THREAD_NETWORK_PRIVILEGED") public void setChannelMaxPowers(@NonNull @Size(min=1) android.util.SparseIntArray, @NonNull java.util.concurrent.Executor, @NonNull android.os.OutcomeReceiver<java.lang.Void,android.net.thread.ThreadNetworkException>);
+    method @FlaggedApi("com.android.net.thread.flags.set_nat64_configuration_enabled") @RequiresPermission(android.Manifest.permission.THREAD_NETWORK_PRIVILEGED) public void setConfiguration(@NonNull android.net.thread.ThreadConfiguration, @NonNull java.util.concurrent.Executor, @NonNull android.os.OutcomeReceiver<java.lang.Void,android.net.thread.ThreadNetworkException>);
     method @RequiresPermission("android.permission.THREAD_NETWORK_PRIVILEGED") public void setEnabled(boolean, @NonNull java.util.concurrent.Executor, @NonNull android.os.OutcomeReceiver<java.lang.Void,android.net.thread.ThreadNetworkException>);
     method @FlaggedApi("com.android.net.thread.flags.configuration_enabled") @RequiresPermission(android.Manifest.permission.THREAD_NETWORK_PRIVILEGED) public void unregisterConfigurationCallback(@NonNull java.util.function.Consumer<android.net.thread.ThreadConfiguration>);
     method @RequiresPermission(allOf={android.Manifest.permission.ACCESS_NETWORK_STATE, "android.permission.THREAD_NETWORK_PRIVILEGED"}) public void unregisterOperationalDatasetCallback(@NonNull android.net.thread.ThreadNetworkController.OperationalDatasetCallback);
diff --git a/thread/framework/java/android/net/thread/ThreadConfiguration.java b/thread/framework/java/android/net/thread/ThreadConfiguration.java
index 1c25535..e6fa1ef 100644
--- a/thread/framework/java/android/net/thread/ThreadConfiguration.java
+++ b/thread/framework/java/android/net/thread/ThreadConfiguration.java
@@ -126,18 +126,29 @@
      *
      * @hide
      */
+    @FlaggedApi(Flags.FLAG_SET_NAT64_CONFIGURATION_ENABLED)
+    @SystemApi
     public static final class Builder {
         private boolean mNat64Enabled = false;
         private boolean mDhcpv6PdEnabled = false;
 
-        /** Creates a new {@link Builder} object with all features disabled. */
+        /**
+         * Creates a new {@link Builder} object with all features disabled.
+         *
+         * @hide
+         */
+        @FlaggedApi(Flags.FLAG_SET_NAT64_CONFIGURATION_ENABLED)
+        @SystemApi
         public Builder() {}
 
         /**
          * Creates a new {@link Builder} object from a {@link ThreadConfiguration} object.
          *
          * @param config the Border Router configurations to be copied
+         * @hide
          */
+        @FlaggedApi(Flags.FLAG_SET_NAT64_CONFIGURATION_ENABLED)
+        @SystemApi
         public Builder(@NonNull ThreadConfiguration config) {
             Objects.requireNonNull(config);
 
@@ -150,7 +161,11 @@
          *
          * <p>Enabling this feature will allow Thread devices to connect to the internet/cloud over
          * IPv4.
+         *
+         * @hide
          */
+        @FlaggedApi(Flags.FLAG_SET_NAT64_CONFIGURATION_ENABLED)
+        @SystemApi
         @NonNull
         public Builder setNat64Enabled(boolean enabled) {
             this.mNat64Enabled = enabled;
@@ -162,6 +177,8 @@
          *
          * <p>Enabling this feature will allow Thread devices to connect to the internet/cloud over
          * IPv6.
+         *
+         * @hide
          */
         @NonNull
         public Builder setDhcpv6PdEnabled(boolean enabled) {
@@ -169,7 +186,13 @@
             return this;
         }
 
-        /** Creates a new {@link ThreadConfiguration} object. */
+        /**
+         * Creates a new {@link ThreadConfiguration} object.
+         *
+         * @hide
+         */
+        @FlaggedApi(Flags.FLAG_SET_NAT64_CONFIGURATION_ENABLED)
+        @SystemApi
         @NonNull
         public ThreadConfiguration build() {
             return new ThreadConfiguration(this);
diff --git a/thread/framework/java/android/net/thread/ThreadNetworkController.java b/thread/framework/java/android/net/thread/ThreadNetworkController.java
index f716f98..6d20e13 100644
--- a/thread/framework/java/android/net/thread/ThreadNetworkController.java
+++ b/thread/framework/java/android/net/thread/ThreadNetworkController.java
@@ -748,15 +748,19 @@
      * OutcomeReceiver#onResult} will be called, and the {@code configuration} will be applied and
      * persisted to the device; the configuration changes can be observed by {@link
      * #registerConfigurationCallback}. On failure, {@link OutcomeReceiver#onError} of {@code
-     * receiver} will be invoked with a specific error.
+     * receiver} will be invoked with a specific error:
+     *
+     * <ul>
+     *   <li>{@link ThreadNetworkException#ERROR_UNSUPPORTED_FEATURE} the configuration enables a
+     *       feature which is not supported by the platform.
+     * </ul>
      *
      * @param configuration the configuration to set
      * @param executor the executor to execute {@code receiver}
      * @param receiver the receiver to receive result of this operation
-     * @hide
      */
-    // @FlaggedApi(ThreadNetworkFlags.FLAG_CONFIGURATION_ENABLED)
-    // @RequiresPermission(permission.THREAD_NETWORK_PRIVILEGED)
+    @FlaggedApi(Flags.FLAG_SET_NAT64_CONFIGURATION_ENABLED)
+    @RequiresPermission(permission.THREAD_NETWORK_PRIVILEGED)
     public void setConfiguration(
             @NonNull ThreadConfiguration configuration,
             @NonNull @CallbackExecutor Executor executor,
diff --git a/thread/service/java/com/android/server/thread/ThreadNetworkControllerService.java b/thread/service/java/com/android/server/thread/ThreadNetworkControllerService.java
index 3d854d7..fa692b0 100644
--- a/thread/service/java/com/android/server/thread/ThreadNetworkControllerService.java
+++ b/thread/service/java/com/android/server/thread/ThreadNetworkControllerService.java
@@ -220,7 +220,6 @@
     private boolean mUserRestricted;
     private boolean mForceStopOtDaemonEnabled;
 
-    private OtDaemonConfiguration mOtDaemonConfig;
     private InfraLinkState mInfraLinkState;
 
     @VisibleForTesting
@@ -249,7 +248,6 @@
         // TODO: networkToLinkProperties should be shared with NsdPublisher, add a test/assert to
         // verify they are the same.
         mNetworkToLinkProperties = networkToLinkProperties;
-        mOtDaemonConfig = new OtDaemonConfiguration.Builder().build();
         mInfraLinkState = new InfraLinkState.Builder().build();
         mPersistentSettings = persistentSettings;
         mNsdPublisher = nsdPublisher;
@@ -346,6 +344,7 @@
         otDaemon.initialize(
                 mTunIfController.getTunFd(),
                 shouldEnableThread(),
+                newOtDaemonConfig(mPersistentSettings.getConfiguration()),
                 mNsdPublisher,
                 getMeshcopTxtAttributes(mResources.get()),
                 mOtDaemonCallbackProxy,
@@ -556,22 +555,21 @@
     public void setConfiguration(
             @NonNull ThreadConfiguration configuration, @NonNull IOperationReceiver receiver) {
         enforceAllPermissionsGranted(PERMISSION_THREAD_NETWORK_PRIVILEGED);
-        mHandler.post(() -> setConfigurationInternal(configuration, receiver));
+        mHandler.post(
+                () ->
+                        setConfigurationInternal(
+                                configuration, new OperationReceiverWrapper(receiver)));
     }
 
     private void setConfigurationInternal(
             @NonNull ThreadConfiguration configuration,
-            @NonNull IOperationReceiver operationReceiver) {
+            @NonNull OperationReceiverWrapper receiver) {
         checkOnHandlerThread();
 
         LOG.i("Set Thread configuration: " + configuration);
 
         final boolean changed = mPersistentSettings.putConfiguration(configuration);
-        try {
-            operationReceiver.onSuccess();
-        } catch (RemoteException e) {
-            // do nothing if the client is dead
-        }
+        receiver.onSuccess();
         if (changed) {
             for (IConfigurationReceiver configReceiver : mConfigurationReceivers.keySet()) {
                 try {
@@ -581,7 +579,22 @@
                 }
             }
         }
-        // TODO: set the configuration at ot-daemon
+        try {
+            getOtDaemon()
+                    .setConfiguration(
+                            newOtDaemonConfig(configuration),
+                            new LoggingOtStatusReceiver("setConfiguration"));
+        } catch (RemoteException | ThreadNetworkException e) {
+            LOG.e("otDaemon.setConfiguration failed. Config: " + configuration, e);
+        }
+    }
+
+    private static OtDaemonConfiguration newOtDaemonConfig(
+            @NonNull ThreadConfiguration threadConfig) {
+        return new OtDaemonConfiguration.Builder()
+                .setNat64Enabled(threadConfig.isNat64Enabled())
+                .setDhcpv6PdEnabled(threadConfig.isDhcpv6PdEnabled())
+                .build();
     }
 
     @Override
@@ -1477,11 +1490,6 @@
         return builder.build();
     }
 
-    private static OtDaemonConfiguration.Builder newOtDaemonConfigBuilder(
-            OtDaemonConfiguration config) {
-        return new OtDaemonConfiguration.Builder();
-    }
-
     private static InfraLinkState.Builder newInfraLinkStateBuilder() {
         return new InfraLinkState.Builder().setInterfaceName("");
     }
diff --git a/thread/tests/cts/src/android/net/thread/cts/ThreadNetworkControllerTest.java b/thread/tests/cts/src/android/net/thread/cts/ThreadNetworkControllerTest.java
index 1792bfb..07438e9 100644
--- a/thread/tests/cts/src/android/net/thread/cts/ThreadNetworkControllerTest.java
+++ b/thread/tests/cts/src/android/net/thread/cts/ThreadNetworkControllerTest.java
@@ -182,6 +182,7 @@
     @After
     public void tearDown() throws Exception {
         dropAllPermissions();
+        setEnabledAndWait(mController, true);
         leaveAndWait(mController);
         tearDownTestNetwork();
         setConfigurationAndWait(mController, DEFAULT_CONFIG);
@@ -1148,15 +1149,9 @@
         CompletableFuture<Void> setFuture2 = new CompletableFuture<>();
         ConfigurationListener listener = new ConfigurationListener(mController);
         ThreadConfiguration config1 =
-                new ThreadConfiguration.Builder()
-                        .setNat64Enabled(true)
-                        .setDhcpv6PdEnabled(true)
-                        .build();
+                new ThreadConfiguration.Builder().setNat64Enabled(true).build();
         ThreadConfiguration config2 =
-                new ThreadConfiguration.Builder()
-                        .setNat64Enabled(false)
-                        .setDhcpv6PdEnabled(true)
-                        .build();
+                new ThreadConfiguration.Builder().setNat64Enabled(false).build();
 
         try {
             runAsShell(
diff --git a/thread/tests/unit/src/com/android/server/thread/ThreadNetworkControllerServiceTest.java b/thread/tests/unit/src/com/android/server/thread/ThreadNetworkControllerServiceTest.java
index b97e2b7..7ac404f 100644
--- a/thread/tests/unit/src/com/android/server/thread/ThreadNetworkControllerServiceTest.java
+++ b/thread/tests/unit/src/com/android/server/thread/ThreadNetworkControllerServiceTest.java
@@ -741,10 +741,7 @@
                         .setDhcpv6PdEnabled(false)
                         .build();
         ThreadConfiguration config2 =
-                new ThreadConfiguration.Builder()
-                        .setNat64Enabled(true)
-                        .setDhcpv6PdEnabled(true)
-                        .build();
+                new ThreadConfiguration.Builder().setNat64Enabled(true).build();
         ThreadConfiguration config3 =
                 new ThreadConfiguration.Builder(config2).build(); // Same as config2