diff --git a/runtime/config-deployer-service/ballerina/APIClient.bal b/runtime/config-deployer-service/ballerina/APIClient.bal
index 72096f208c..174b57dca5 100644
--- a/runtime/config-deployer-service/ballerina/APIClient.bal
+++ b/runtime/config-deployer-service/ballerina/APIClient.bal
@@ -361,9 +361,17 @@ public class APIClient {
                 authTypes.jwt = {header: <string>jwtAuthentication.headerName, sendTokenToUpstream: <boolean>jwtAuthentication.sendTokenToUpstream, disabled: !jwtAuthentication.enabled, audience: jwtAuthentication.audience};
             } else if authentication.authType == "APIKey" && authentication is APIKeyAuthentication {
                 APIKeyAuthentication apiKeyAuthentication = check authentication.cloneWithType(APIKeyAuthentication);
-                authTypes.apiKey = [];
-                authTypes.apiKey.push({'in: "Header", name: apiKeyAuthentication.headerName, sendTokenToUpstream: apiKeyAuthentication.sendTokenToUpstream});
-                authTypes.apiKey.push({'in: "Query", name: apiKeyAuthentication.queryParamName, sendTokenToUpstream: apiKeyAuthentication.sendTokenToUpstream});
+                model:APIKey[] apiKeys = [];
+                boolean|() headerEnabled = apiKeyAuthentication.headerEnable;
+                boolean|() queryEnabled = apiKeyAuthentication.queryParamEnable;
+
+                if headerEnabled is boolean && headerEnabled {
+                    apiKeys.push({'in: "Header", name: <string>apiKeyAuthentication.headerName, sendTokenToUpstream: apiKeyAuthentication.sendTokenToUpstream});
+                }
+                if queryEnabled is boolean && queryEnabled {
+                    apiKeys.push({'in: "Query", name: <string>apiKeyAuthentication.queryParamName, sendTokenToUpstream: apiKeyAuthentication.sendTokenToUpstream});
+                }
+                authTypes.apiKey = apiKeys;
             } else if authentication.authType == "mTLS" {
                 MTLSAuthentication mtlsAuthentication = check authentication.cloneWithType(MTLSAuthentication);
                 isMTLSMandatory = mtlsAuthentication.required == "mandatory";
diff --git a/runtime/config-deployer-service/ballerina/types.bal b/runtime/config-deployer-service/ballerina/types.bal
index 66d04272f4..90f428ffaa 100644
--- a/runtime/config-deployer-service/ballerina/types.bal
+++ b/runtime/config-deployer-service/ballerina/types.bal
@@ -275,8 +275,8 @@ public type APIKeyAuthentication record {|
     boolean sendTokenToUpstream = false;
     string headerName = "apiKey";
     string queryParamName = "apiKey";
-    boolean headerEnable = true;
-    boolean queryParamEnable = true;
+    boolean headerEnable?;
+    boolean queryParamEnable?;
 |};
 
 # Mutual SSL configuration of this API