diff --git a/thread/tests/integration/src/android/net/thread/BorderRoutingTest.java b/thread/tests/integration/src/android/net/thread/BorderRoutingTest.java
index cf7a4f753e..f8e92f0766 100644
--- a/thread/tests/integration/src/android/net/thread/BorderRoutingTest.java
+++ b/thread/tests/integration/src/android/net/thread/BorderRoutingTest.java
@@ -650,9 +650,8 @@ public class BorderRoutingTest {
     public void nat64_threadDevicePingIpv4InfraDevice_outboundPacketIsForwarded() throws Exception {
         FullThreadDevice ftd = mFtds.get(0);
         joinNetworkAndWaitForOmr(ftd, DEFAULT_DATASET);
-        // TODO: enable NAT64 via ThreadNetworkController API instead of ot-ctl
         mOtCtl.setNat64Cidr(NAT64_CIDR);
-        mOtCtl.setNat64Enabled(true);
+        mController.setNat64EnabledAndWait(true);
         waitFor(() -> mOtCtl.hasNat64PrefixInNetdata(), UPDATE_NAT64_PREFIX_TIMEOUT);
 
         ftd.ping(IPV4_SERVER_ADDR);
@@ -685,8 +684,7 @@ public class BorderRoutingTest {
         mInfraNetworkReader = newPacketReader(mInfraNetworkTracker.getTestIface(), mHandler);
         FullThreadDevice ftd = mFtds.get(0);
         joinNetworkAndWaitForOmr(ftd, DEFAULT_DATASET);
-        // TODO: enable NAT64 via ThreadNetworkController API instead of ot-ctl
-        mOtCtl.setNat64Enabled(true);
+        mController.setNat64EnabledAndWait(true);
         mOtCtl.addPrefixInNetworkData(DHCP6_PD_PREFIX, "paros", "med");
         waitFor(() -> mOtCtl.hasNat64PrefixInNetdata(), UPDATE_NAT64_PREFIX_TIMEOUT);
 
diff --git a/thread/tests/integration/src/android/net/thread/utils/ThreadNetworkControllerWrapper.java b/thread/tests/integration/src/android/net/thread/utils/ThreadNetworkControllerWrapper.java
index 4a30c45da0..295acb8ff6 100644
--- a/thread/tests/integration/src/android/net/thread/utils/ThreadNetworkControllerWrapper.java
+++ b/thread/tests/integration/src/android/net/thread/utils/ThreadNetworkControllerWrapper.java
@@ -200,7 +200,7 @@ public final class ThreadNetworkControllerWrapper {
         runAsShell(
                 PERMISSION_THREAD_NETWORK_PRIVILEGED,
                 () -> mController.registerConfigurationCallback(directExecutor(), callback));
-        future.get(CALLBACK_TIMEOUT.toSeconds(), SECONDS);
+        future.get(CONFIG_TIMEOUT.toSeconds(), SECONDS);
         runAsShell(
                 PERMISSION_THREAD_NETWORK_PRIVILEGED,
                 () -> mController.unregisterConfigurationCallback(callback));
@@ -214,7 +214,14 @@ public final class ThreadNetworkControllerWrapper {
                 () ->
                         mController.setConfiguration(
                                 config, directExecutor(), newOutcomeReceiver(future)));
-        future.get(CALLBACK_TIMEOUT.toSeconds(), SECONDS);
+        future.get(CONFIG_TIMEOUT.toSeconds(), SECONDS);
+    }
+
+    public void setNat64EnabledAndWait(boolean enabled) throws Exception {
+        final ThreadConfiguration config = getConfiguration();
+        final ThreadConfiguration newConfig =
+                new ThreadConfiguration.Builder().setNat64Enabled(enabled).build();
+        setConfigurationAndWait(newConfig);
     }
 
     private static <V> OutcomeReceiver<V, ThreadNetworkException> newOutcomeReceiver(