diff --git a/setup.cfg b/setup.cfg
index 5aafd280bcee..75c0c8c87f10 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,5 +1,4 @@
 [tool:pytest]
-testpaths = tests
 addopts = -rfEs
 norecursedirs = *.egg-info .git .mypy_cache node_modules .pytest_cache .vscode
 
diff --git a/src/prefect/runner/runner.py b/src/prefect/runner/runner.py
index dbdca6ad6fdb..97b250ca42ee 100644
--- a/src/prefect/runner/runner.py
+++ b/src/prefect/runner/runner.py
@@ -78,9 +78,7 @@ def fast_flow():
 )
 from prefect.deployments.schedules import FlexibleScheduleList
 from prefect.events import DeploymentTriggerTypes, TriggerTypes
-from prefect.exceptions import (
-    Abort,
-)
+from prefect.exceptions import Abort, ObjectNotFound
 from prefect.flows import Flow
 from prefect.logging.loggers import PrefectLogAdapter, flow_run_logger, get_logger
 from prefect.runner.server import start_webserver
@@ -1130,12 +1128,18 @@ async def _run_on_cancellation_hooks(
         Run the hooks for a flow.
         """
         if state.is_cancelling():
-            flow = await load_flow_from_flow_run(
-                flow_run, client=self._client, storage_base_path=str(self._tmp_dir)
-            )
-            hooks = flow.on_cancellation or []
+            try:
+                flow = await load_flow_from_flow_run(
+                    flow_run, client=self._client, storage_base_path=str(self._tmp_dir)
+                )
+                hooks = flow.on_cancellation or []
 
-            await _run_hooks(hooks, flow_run, flow, state)
+                await _run_hooks(hooks, flow_run, flow, state)
+            except ObjectNotFound:
+                run_logger = self._get_flow_run_logger(flow_run)
+                run_logger.warning(
+                    f"Runner cannot retrieve flow to execute cancellation hooks for flow run {flow_run.id!r}."
+                )
 
     async def _run_on_crashed_hooks(
         self,
diff --git a/tests/runner/test_runner.py b/tests/runner/test_runner.py
index dd00cb8c4caa..37a4fd844401 100644
--- a/tests/runner/test_runner.py
+++ b/tests/runner/test_runner.py
@@ -474,6 +474,83 @@ def cancel_flow(sleep_time: int = 100):
         # check to make sure on_cancellation hook was called
         assert "This flow was cancelled!" in caplog.text
 
+    @pytest.mark.usefixtures("use_hosted_api_server")
+    async def test_runner_warns_if_unable_to_load_cancellation_hooks(
+        self,
+        prefect_client: PrefectClient,
+        caplog: pytest.LogCaptureFixture,
+        in_temporary_runner_directory: None,
+        temp_storage: MockStorage,
+    ):
+        runner = Runner(query_seconds=2)
+
+        temp_storage.code = dedent(
+            """\
+            from time import sleep
+            from prefect import flow
+            from prefect.logging.loggers import flow_run_logger
+            def on_cancellation(flow, flow_run, state):
+                logger = flow_run_logger(flow_run, flow)
+                logger.info("This flow was cancelled!")
+            @flow(on_cancellation=[on_cancellation], log_prints=True)
+            def cancel_flow(sleep_time: int = 100):
+                sleep(sleep_time)
+            """
+        )
+
+        deployment_id = await runner.add_flow(
+            await flow.from_source(
+                source=temp_storage, entrypoint="flows.py:cancel_flow"
+            ),
+            name=__file__,
+        )
+
+        async with anyio.create_task_group() as tg:
+            tg.start_soon(runner.start)
+
+            flow_run = await prefect_client.create_flow_run_from_deployment(
+                deployment_id=deployment_id
+            )
+
+            # Need to wait for polling loop to pick up flow run and
+            # start execution
+            while True:
+                await anyio.sleep(0.5)
+                flow_run = await prefect_client.read_flow_run(flow_run_id=flow_run.id)
+                assert flow_run.state
+                if flow_run.state.is_running():
+                    break
+
+            await prefect_client.delete_deployment(deployment_id=deployment_id)
+
+            await prefect_client.set_flow_run_state(
+                flow_run_id=flow_run.id,
+                state=flow_run.state.copy(
+                    update={"name": "Cancelling", "type": StateType.CANCELLING}
+                ),
+            )
+
+            # Need to wait for polling loop to pick up flow run and then
+            # finish cancellation
+            while True:
+                await anyio.sleep(0.5)
+                flow_run = await prefect_client.read_flow_run(flow_run_id=flow_run.id)
+                assert flow_run.state
+                if flow_run.state.is_cancelled():
+                    break
+
+            await runner.stop()
+            tg.cancel_scope.cancel()
+
+        # Cancellation hook should not have been called successfully
+        # but the flow run should still be cancelled correctly
+        assert flow_run.state.is_cancelled()
+        assert "This flow was cancelled!" not in caplog.text
+        assert (
+            "Runner cannot retrieve flow to execute cancellation hooks for flow run"
+            in caplog.text
+        )
+
     @pytest.mark.usefixtures("use_hosted_api_server")
     async def test_runner_runs_on_crashed_hooks_for_remotely_stored_flows(
         self,