diff --git a/lib/galaxy/tool_util/linters/outputs.py b/lib/galaxy/tool_util/linters/outputs.py
index 8232cbab891f..e3de862b8836 100644
--- a/lib/galaxy/tool_util/linters/outputs.py
+++ b/lib/galaxy/tool_util/linters/outputs.py
@@ -45,7 +45,14 @@ def lint_output(tool_xml, lint_ctx):
 
         label = output.attrib.get("label", "${tool.name} on ${on_string}")
         if label in labels:
-            lint_ctx.error(f"Tool output [{name}] uses duplicated label '{label}'", node=output)
+            filter_node = output.find(".//filter")
+            if filter_node is not None:
+                lint_ctx.warn(
+                    f"Tool output [{name}] uses duplicated label '{label}', double check if filters imply disjoint cases",
+                    node=output,
+                )
+            else:
+                lint_ctx.warn(f"Tool output [{name}] uses duplicated label '{label}'", node=output)
         labels.add(label)
 
         format_set = False
diff --git a/test/unit/tool_util/test_tool_linters.py b/test/unit/tool_util/test_tool_linters.py
index f2b2db004df0..e9ea77589cfd 100644
--- a/test/unit/tool_util/test_tool_linters.py
+++ b/test/unit/tool_util/test_tool_linters.py
@@ -566,6 +566,12 @@
     <outputs>
         <data name="valid_name" format="fasta"/>
         <data name="valid_name" format="fasta"/>
+        <data name="another_valid_name" format="fasta" label="same label may be OK if there is a filter">
+            <filter>a condition</filter>
+        </data>
+        <data name="yet_another_valid_name" format="fasta" label="same label may be OK if there is a filter">
+            <filter>another condition</filter>
+        </data>
     </outputs>
 </tool>
 """
@@ -1492,13 +1498,17 @@ def test_outputs_discover_tool_provided_metadata(lint_ctx):
 def test_outputs_duplicated_name_label(lint_ctx):
     tool_source = get_xml_tool_source(OUTPUTS_DUPLICATED_NAME_LABEL)
     run_lint(lint_ctx, outputs.lint_output, tool_source)
-    assert "2 outputs found." in lint_ctx.info_messages
+    assert "4 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 len(lint_ctx.warn_messages) == 2
+    assert "Tool output [valid_name] uses duplicated label '${tool.name} on ${on_string}'" in lint_ctx.warn_messages
+    assert (
+        "Tool output [yet_another_valid_name] uses duplicated label 'same label may be OK if there is a filter', double check if filters imply disjoint cases"
+        in lint_ctx.warn_messages
+    )
     assert "Tool output [valid_name] has duplicated name" in lint_ctx.error_messages
-    assert "Tool output [valid_name] uses duplicated label '${tool.name} on ${on_string}'" in lint_ctx.error_messages
-    assert len(lint_ctx.error_messages) == 2
+    assert len(lint_ctx.error_messages) == 1
 
 
 def test_stdio_default_for_default_profile(lint_ctx):