diff --git a/cylc/flow/config.py b/cylc/flow/config.py
index 5b7738f3e6c..d29537ce7ab 100644
--- a/cylc/flow/config.py
+++ b/cylc/flow/config.py
@@ -2434,9 +2434,18 @@ def get_taskdef(
                 raise WorkflowConfigError(str(exc))
             else:
                 # Record custom message outputs from [runtime].
+                messages = set(self.cfg['runtime'][name]['outputs'].values())
                 for output, message in (
                     self.cfg['runtime'][name]['outputs'].items()
                 ):
+                    try:
+                        messages.remove(message)
+                    except KeyError:
+                        raise WorkflowConfigError(
+                            'Duplicate task message in'
+                            f' "[runtime][{name}][outputs]'
+                            f'{output} = {message}" - messages must be unique'
+                        )
                     valid, msg = TaskOutputValidator.validate(output)
                     if not valid:
                         raise WorkflowConfigError(
diff --git a/tests/integration/validate/test_outputs.py b/tests/integration/validate/test_outputs.py
index b26bce529fb..1a8177cd35b 100644
--- a/tests/integration/validate/test_outputs.py
+++ b/tests/integration/validate/test_outputs.py
@@ -339,3 +339,37 @@ def test_completion_expression_cylc7_compat(
         match="completion cannot be used in Cylc 7 compatibility mode."
     ):
         validate(id_)
+
+
+def test_unique_messages(
+    flow,
+    validate
+):
+    """Task messages must be unique in the [outputs] section.
+
+    See: https://github.com/cylc/cylc-flow/issues/6056
+    """
+    id_ = flow({
+        'scheduling': {
+            'graph': {'R1': 'foo'}
+        },
+        'runtime': {
+            'foo': {
+                'outputs': {
+                    'a': 'foo',
+                    'b': 'bar',
+                    'c': 'baz',
+                    'd': 'foo',
+                }
+            },
+        }
+    })
+
+    with pytest.raises(
+        WorkflowConfigError,
+        match=(
+            r'"\[runtime\]\[foo\]\[outputs\]d = foo"'
+            ' - messages must be unique'
+        ),
+    ):
+        validate(id_)