diff --git a/tools/make_makefiles b/tools/make_makefiles
index 78b6deaef7b..e65429f60ff 100755
--- a/tools/make_makefiles
+++ b/tools/make_makefiles
@@ -202,7 +202,7 @@ sub parse_makefile($)
 
         if (/\@[A-Z_]+\@/)  # config.status substitution variable
         {
-            die "Configure substitution is not allowed in $file";
+            die "Configure substitution is not allowed in $file" unless $file eq "Makefile";
         }
         if (/^\s*(MODULE|IMPORTLIB|TESTDLL|PARENTSRC|APPMODE)\s*=\s*(.*)/)
         {