diff --git a/lib/galaxy/tool_util/linters/output.py b/lib/galaxy/tool_util/linters/output.py
index 6323865db868..e9ab7c4aaf4e 100644
--- a/lib/galaxy/tool_util/linters/output.py
+++ b/lib/galaxy/tool_util/linters/output.py
@@ -87,7 +87,7 @@ def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
             try:
                 ast.parse(filter.text, mode="eval")
             except Exception as e:
-                lint_ctx.error(
+                lint_ctx.warn(
                     f"Filter '{filter.text}' is no valid expression: {str(e)}",
                     linter=cls.name(),
                     node=filter,
diff --git a/test/unit/tool_util/test_tool_linters.py b/test/unit/tool_util/test_tool_linters.py
index 2db8cca0abfd..fc99e74ed963 100644
--- a/test/unit/tool_util/test_tool_linters.py
+++ b/test/unit/tool_util/test_tool_linters.py
@@ -1753,16 +1753,16 @@ def test_outputs_filter_expression(lint_ctx):
     assert "2 outputs found." in lint_ctx.info_messages
     assert len(lint_ctx.info_messages) == 1
     assert not lint_ctx.valid_messages
-    assert not lint_ctx.warn_messages
     assert (
         "Filter 'another invalid condition' is no valid expression: invalid syntax (<unknown>, line 1)"
-        in lint_ctx.error_messages
+        in lint_ctx.warn_messages
     )
     assert (
         "Filter 'another invalid condition' is no valid expression: invalid syntax (<unknown>, line 1)"
-        in lint_ctx.error_messages
+        in lint_ctx.warn_messages
     )
-    assert len(lint_ctx.error_messages) == 2
+    assert len(lint_ctx.warn_messages) == 2
+    assert not lint_ctx.error_messages
 
 
 def test_stdio_default_for_default_profile(lint_ctx):