diff --git a/setup.py b/setup.py
index 1748781985f..b0cca73bb91 100644
--- a/setup.py
+++ b/setup.py
@@ -693,6 +693,12 @@ class precompiled_wheel_utils:
                 flash_attn_regex = re.compile(
                     r"vllm/vllm_flash_attn/(?:[^/.][^/]*/)*(?!\.)[^/]*\.py"
                 )
+                # __init__.py and flash_attn_interface.py are source-controlled
+                # in vllm and should not be overwritten (matches cmake exclusions)
+                flash_attn_files_to_skip = {
+                    "vllm/vllm_flash_attn/__init__.py",
+                    "vllm/vllm_flash_attn/flash_attn_interface.py",
+                }
                 triton_kernels_regex = re.compile(
                     r"vllm/third_party/triton_kernels/(?:[^/.][^/]*/)*(?!\.)[^/]*\.py"
                 )
@@ -705,7 +711,11 @@ class precompiled_wheel_utils:
                     filter(lambda x: x.filename in files_to_copy, wheel.filelist)
                 )
                 file_members += list(
-                    filter(lambda x: flash_attn_regex.match(x.filename), wheel.filelist)
+                    filter(
+                        lambda x: flash_attn_regex.match(x.filename)
+                        and x.filename not in flash_attn_files_to_skip,
+                        wheel.filelist,
+                    )
                 )
                 file_members += list(
                     filter(