diff --git a/build/gen.py b/build/gen.py
index d2305c8f..811c2e95 100755
--- a/build/gen.py
+++ b/build/gen.py
@@ -324,8 +324,11 @@ def WriteGNNinja(path, platform, host, options):
         ldflags.append('-Wl,--icf=all')
 
       if options.use_lto:
-        cflags.extend(['-flto', '-fwhole-program-vtables'])
-        ldflags.extend(['-flto', '-fwhole-program-vtables'])
+        cflags.append('-flto')
+        ldflags.append('-flto')
+        if "clang" in cxx:
+          cflags.append('-fwhole-program-vtables')
+          ldflags.append('-fwhole-program-vtables')
 
     cflags.extend([
         '-D_FILE_OFFSET_BITS=64',