diff --git a/tools/aapt2/cmd/Link.cpp b/tools/aapt2/cmd/Link.cpp
index 24699bf..c739d77 100644
--- a/tools/aapt2/cmd/Link.cpp
+++ b/tools/aapt2/cmd/Link.cpp
@@ -1987,6 +1987,8 @@
     context_->SetNameManglerPolicy(NameManglerPolicy{context_->GetCompilationPackage()});
     context_->SetSplitNameDependencies(app_info_.split_name_dependencies);
 
+    std::unique_ptr<xml::XmlResource> pre_flags_filter_manifest_xml = manifest_xml->Clone();
+
     FeatureFlagsFilterOptions flags_filter_options;
     if (context_->GetMinSdkVersion() > SDK_UPSIDE_DOWN_CAKE) {
       // For API version > U, PackageManager will dynamically read the flag values and disable
@@ -2296,7 +2298,12 @@
         }
 
         if (options_.generate_java_class_path) {
-          if (!WriteManifestJavaFile(manifest_xml.get())) {
+          // The FeatureFlagsFilter may remove <permission> and <permission-group> elements that
+          // generate constants in the Manifest Java file. While we want those permissions and
+          // permission groups removed in the SDK (i.e., if a feature flag is disabled), the
+          // constants should still remain so that code referencing it (e.g., within a feature
+          // flag check) will still compile. Therefore we use the manifest XML before the filter.
+          if (!WriteManifestJavaFile(pre_flags_filter_manifest_xml.get())) {
             error = true;
           }
         }
diff --git a/tools/aapt2/cmd/Link_test.cpp b/tools/aapt2/cmd/Link_test.cpp
index 7ceb351..10d0b1f 100644
--- a/tools/aapt2/cmd/Link_test.cpp
+++ b/tools/aapt2/cmd/Link_test.cpp
@@ -1021,9 +1021,11 @@
                           .AddContents(manifest_contents)
                           .Build();
 
+  const std::string app_java = GetTestPath("app-java");
   auto app_link_args = LinkCommandBuilder(this)
                            .SetManifestFile(app_manifest)
                            .AddParameter("-I", android_apk)
+                           .AddParameter("--java", app_java)
                            .AddParameter("--feature-flags", "flag=false");
 
   const std::string app_apk = GetTestPath("app.apk");
@@ -1038,6 +1040,12 @@
   ASSERT_THAT(root, NotNull());
   auto maybe_removed = root->FindChild({}, "permission");
   ASSERT_THAT(maybe_removed, IsNull());
+
+  // Code for the permission should be generated even if the element is removed
+  const std::string manifest_java = app_java + "/com/example/app/Manifest.java";
+  std::string manifest_java_contents;
+  ASSERT_TRUE(android::base::ReadFileToString(manifest_java, &manifest_java_contents));
+  EXPECT_THAT(manifest_java_contents, HasSubstr(" public static final String FOO=\"FOO\";"));
 }
 
 TEST_F(LinkTest, FeatureFlagEnabled_SdkAtMostUDC) {