diff --git a/src/coreclr/nativeaot/BuildIntegration/Microsoft.DotNet.ILCompiler.SingleEntry.targets b/src/coreclr/nativeaot/BuildIntegration/Microsoft.DotNet.ILCompiler.SingleEntry.targets
index 1b3d56e863c3fc..e8a66c5f2419ea 100644
--- a/src/coreclr/nativeaot/BuildIntegration/Microsoft.DotNet.ILCompiler.SingleEntry.targets
+++ b/src/coreclr/nativeaot/BuildIntegration/Microsoft.DotNet.ILCompiler.SingleEntry.targets
@@ -48,7 +48,8 @@
   <!-- Generate a warning if the non-SDK path is used  -->
   <Target Name="GenerateILCompilerExplicitPackageReferenceWarning" Condition="'$(SuppressGenerateILCompilerExplicitPackageReferenceWarning)' == '' and '$(AotRuntimePackageLoadedViaSDK)' != 'true' and '$(ILCompilerTargetsPath)' != ''  and '$(NeedNativePublishSupportForSDK6)' != 'true'" 
       BeforeTargets="ImportRuntimeIlcPackageTarget">
-    <Warning Text="Delete explicit 'Microsoft.DotNet.ILCompiler' package reference in your project file. Explicit 'Microsoft.DotNet.ILCompiler' package reference can run into version errors." />
+    <Warning Condition="'%(PackageReference.Identity)' == 'Microsoft.DotNet.ILCompiler' And '%(PackageReference.IsImplicitlyDefined)' != 'true'"
+             Text="Delete explicit 'Microsoft.DotNet.ILCompiler' package reference in your project file. Explicit 'Microsoft.DotNet.ILCompiler' package reference can run into version errors." />
   </Target>
 
   <!-- Locate the runtime package according to the current target runtime -->