diff --git a/pyproject.toml b/pyproject.toml
index 684d905002..f7a38926b2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -292,6 +292,8 @@ exclude = '''
 [tool.ruff]
 line-length = 120
 target-version = "py310"
+# .pre-commit-config.yaml's ruff hook excludes these separately at the pre-commit layer
+extend-exclude = ["versioneer.py", "monai/_version.py"]
 
 [tool.ruff.lint]
 select = [
diff --git a/runtests.sh b/runtests.sh
index 0fc18b36ec..af1835c11d 100755
--- a/runtests.sh
+++ b/runtests.sh
@@ -599,9 +599,9 @@ then
 
     if [ $doRuffFix = true ]
     then
-        ruff check --fix --unsafe-fixes --exclude versioneer.py --exclude "monai/_version.py" "$homedir"
+        ruff check --fix --unsafe-fixes "$homedir"
     else
-        ruff check --exclude versioneer.py --exclude "monai/_version.py" "$homedir"
+        ruff check "$homedir"
     fi
 
     ruff_status=$?