diff --git a/modules/integration/tests-integration/tests-backend/src/test/java/org/wso2/identity/integration/test/applicationNativeAuthentication/ApplicationNativeAuthenticationTestCase.java b/modules/integration/tests-integration/tests-backend/src/test/java/org/wso2/identity/integration/test/applicationNativeAuthentication/ApplicationNativeAuthenticationTestCase.java
index fe2694f6cd5..e156721a136 100644
--- a/modules/integration/tests-integration/tests-backend/src/test/java/org/wso2/identity/integration/test/applicationNativeAuthentication/ApplicationNativeAuthenticationTestCase.java
+++ b/modules/integration/tests-integration/tests-backend/src/test/java/org/wso2/identity/integration/test/applicationNativeAuthentication/ApplicationNativeAuthenticationTestCase.java
@@ -49,6 +49,9 @@
 import org.wso2.identity.integration.test.rest.api.server.application.management.v1.model.ApplicationModel;
 import org.wso2.identity.integration.test.rest.api.server.application.management.v1.model.ApplicationPatchModel;
 import org.wso2.identity.integration.test.rest.api.server.application.management.v1.model.ApplicationResponseModel;
+import org.wso2.identity.integration.test.rest.api.server.application.management.v1.model.AuthenticationSequence;
+import org.wso2.identity.integration.test.rest.api.server.application.management.v1.model.AuthenticationStep;
+import org.wso2.identity.integration.test.rest.api.server.application.management.v1.model.Authenticator;
 import org.wso2.identity.integration.test.rest.api.server.application.management.v1.model.InboundProtocols;
 import org.wso2.identity.integration.test.rest.api.server.application.management.v1.model.OpenIDConnectConfiguration;
 import org.wso2.identity.integration.test.utils.OAuth2Constant;
@@ -66,6 +69,7 @@
 import static org.wso2.identity.integration.test.applicationNativeAuthentication.Constants.AUTHENTICATOR_ID;
 import static org.wso2.identity.integration.test.applicationNativeAuthentication.Constants.AUTH_DATA_CODE;
 import static org.wso2.identity.integration.test.applicationNativeAuthentication.Constants.AUTH_DATA_SESSION_STATE;
+import static org.wso2.identity.integration.test.applicationNativeAuthentication.Constants.BASIC_AUTHENTICATOR;
 import static org.wso2.identity.integration.test.applicationNativeAuthentication.Constants.CODE;
 import static org.wso2.identity.integration.test.applicationNativeAuthentication.Constants.CONTENT_TYPE_APPLICATION_JSON;
 import static org.wso2.identity.integration.test.applicationNativeAuthentication.Constants.ERROR_CODE_CLIENT_NATIVE_AUTHENTICATION_DISABLED;
@@ -75,6 +79,7 @@
 import static org.wso2.identity.integration.test.applicationNativeAuthentication.Constants.HREF;
 import static org.wso2.identity.integration.test.applicationNativeAuthentication.Constants.IDP;
 import static org.wso2.identity.integration.test.applicationNativeAuthentication.Constants.LINKS;
+import static org.wso2.identity.integration.test.applicationNativeAuthentication.Constants.LOCAL;
 import static org.wso2.identity.integration.test.applicationNativeAuthentication.Constants.METADATA;
 import static org.wso2.identity.integration.test.applicationNativeAuthentication.Constants.NEXT_STEP;
 import static org.wso2.identity.integration.test.applicationNativeAuthentication.Constants.PARAMS;
@@ -110,6 +115,7 @@ public class ApplicationNativeAuthenticationTestCase extends OAuth2ServiceAbstra
     private CloseableHttpClient client;
     private UserManagementClient userMgtServiceClient;
     private String code;
+    private static final String basicAuthenticatorId = "QmFzaWNBdXRoZW50aWNhdG9yOkxPQ0FM";
 
     @BeforeClass(alwaysRun = true)
     public void testInit() throws Exception {
@@ -274,6 +280,22 @@ private ApplicationResponseModel createAppWithoutClientNativeAuthentication() th
         application.setInboundProtocolConfiguration(inboundProtocolsConfig);
         application.setName(TEST_APP_NAME);
 
+        // Set Basic authenticator as 1st step.
+        List<Authenticator> authenticators = new ArrayList<>();
+        List<AuthenticationStep> authenticationSteps = new ArrayList<>();
+        Authenticator basicAuthenticator = new Authenticator()
+                .idp(LOCAL)
+                .authenticator(BASIC_AUTHENTICATOR);
+        authenticators.add(basicAuthenticator);
+        AuthenticationSequence authenticationSequence = new AuthenticationSequence();
+        authenticationSequence.setType(AuthenticationSequence.TypeEnum.USER_DEFINED);
+        AuthenticationStep authenticationStep = new AuthenticationStep();
+        authenticationStep.setId(1);
+        authenticationStep.setOptions(authenticators);
+        authenticationSteps.add(authenticationStep);
+        authenticationSequence.setSteps(authenticationSteps);
+        application.setAuthenticationSequence(authenticationSequence);
+
         String appId = addApplication(application);
         return getApplication(appId);
     }
@@ -325,6 +347,8 @@ private void validInitClientNativeAuthnResponse(JSONObject json) {
                             authenticator.containsKey(REQUIRED_PARAMS)) {
 
                         authenticatorId = (String) authenticator.get(AUTHENTICATOR_ID);
+                        Assert.assertEquals(authenticatorId, basicAuthenticatorId, "Authenticator Id is not " +
+                                "equal for basic authenticator ID");
                         JSONObject metadataNode = (JSONObject) authenticator.get(METADATA);
                         if (metadataNode.containsKey(PROMPT_TYPE) && metadataNode.containsKey(PARAMS)) {
                             paramsArray = (JSONArray) metadataNode.get(PARAMS);
diff --git a/modules/integration/tests-integration/tests-backend/src/test/java/org/wso2/identity/integration/test/applicationNativeAuthentication/Constants.java b/modules/integration/tests-integration/tests-backend/src/test/java/org/wso2/identity/integration/test/applicationNativeAuthentication/Constants.java
index 63ce5c8214a..c6e322b9ae7 100644
--- a/modules/integration/tests-integration/tests-backend/src/test/java/org/wso2/identity/integration/test/applicationNativeAuthentication/Constants.java
+++ b/modules/integration/tests-integration/tests-backend/src/test/java/org/wso2/identity/integration/test/applicationNativeAuthentication/Constants.java
@@ -31,6 +31,10 @@ public class Constants {
     public static final String TEST_USER_NAME = "attestationTestUser";
     public static final String TEST_APP_NAME = "oauthTestANAApplication";
 
+    // Basic Authenticator
+    public static final String LOCAL = "LOCAL";
+    public static final String BASIC_AUTHENTICATOR = "BasicAuthenticator";
+
     public static final String TEST_PASSWORD = "passWord1@";
     public static final String TEST_PROFILE = "default";
 
diff --git a/modules/integration/tests-integration/tests-backend/src/test/resources/testng.xml b/modules/integration/tests-integration/tests-backend/src/test/resources/testng.xml
index 5ac345d3acc..9909e125ed8 100644
--- a/modules/integration/tests-integration/tests-backend/src/test/resources/testng.xml
+++ b/modules/integration/tests-integration/tests-backend/src/test/resources/testng.xml
@@ -133,8 +133,7 @@
             <class name="org.wso2.identity.integration.test.identityServlet.ExtendSessionEndpointAuthCodeGrantTestCase"/>
             <class name="org.wso2.identity.integration.test.oauth2.OAuth2TokenRevocationWithSessionTerminationTestCase"/>
             <class name="org.wso2.identity.integration.test.oauth2.OAuth2TokenRevocationWithMultipleSessionTerminationTestCase"/>
-<!--            Temporarily commenting out following test case cause due to intermittent error-->
-<!--            <class name="org.wso2.identity.integration.test.applicationNativeAuthentication.ApplicationNativeAuthenticationTestCase"/>-->
+            <class name="org.wso2.identity.integration.test.applicationNativeAuthentication.ApplicationNativeAuthenticationTestCase"/>
         </classes>
     </test>