diff --git a/doc/versionHistory.rst b/doc/versionHistory.rst
index 7ba087a1..1fb38eda 100644
--- a/doc/versionHistory.rst
+++ b/doc/versionHistory.rst
@@ -6,6 +6,15 @@
 Version History
 ##################
 
+.. _lsst.ts.wep-9.5.5:
+
+-------------
+9.5.5
+-------------
+
+* Correct indices used to calculate Zernike average.
+* Update tests to discern whether flags and mean use the same indices.
+
 .. _lsst.ts.wep-9.5.4:
 
 -------------
diff --git a/python/lsst/ts/wep/task/combineZernikesSigmaClipTask.py b/python/lsst/ts/wep/task/combineZernikesSigmaClipTask.py
index c3d857f6..8a034fe3 100644
--- a/python/lsst/ts/wep/task/combineZernikesSigmaClipTask.py
+++ b/python/lsst/ts/wep/task/combineZernikesSigmaClipTask.py
@@ -77,10 +77,29 @@ def combineZernikes(self, zernikeArray):
         # Create a binary flag array that indicates
         # donuts have outlier values. This array is 1 if
         # it has any outlier values.
-        binaryFlagArray = np.any(
-            np.isnan(sigArray[:, : self.maxZernClip]), axis=1
-        ).astype(int)
+        # If all available donuts have a clipped value in the
+        # first maxZernClip coefficients then reduce maxZernClip by 1
+        # until we get one that passes.
+        numRejected = len(sigArray)
+        effMaxZernClip = self.maxZernClip + 1
+
+        while numRejected == len(sigArray):
+            effMaxZernClip -= 1
+            binaryFlagArray = np.any(
+                np.isnan(sigArray[:, :effMaxZernClip]), axis=1
+            ).astype(int)
+            numRejected = np.sum(binaryFlagArray)
         # Identify which rows to use when calculating final mean
-        keepIdx = ~np.any(np.isnan(sigArray), axis=1)
+        keepIdx = ~np.array(binaryFlagArray, dtype=bool)
+
+        self.log.info(
+            f"MaxZernClip config: {self.maxZernClip}. MaxZernClip used: {effMaxZernClip}."
+        )
+        if effMaxZernClip < self.maxZernClip:
+            self.log.warning(
+                f"EffMaxZernClip ({effMaxZernClip}) was less than MaxZernClip config ({self.maxZernClip})."
+            )
+        self.metadata["maxZernClip"] = self.maxZernClip
+        self.metadata["effMaxZernClip"] = effMaxZernClip
 
         return np.mean(zernikeArray[keepIdx], axis=0), binaryFlagArray
diff --git a/tests/task/test_combineZernikesSigmaClipTask.py b/tests/task/test_combineZernikesSigmaClipTask.py
index 8e2ee18f..29777620 100644
--- a/tests/task/test_combineZernikesSigmaClipTask.py
+++ b/tests/task/test_combineZernikesSigmaClipTask.py
@@ -71,7 +71,7 @@ def testCombineZernikes(self):
         # Test that zernikes higher than maxZernClip don't remove
         # a row from the final averaging
         zernikeArray[0, 3:] += 100.0
-        zernikeArray[51, 3:] -= 100.0
+        zernikeArray[49, 3:] -= 100.0
         # Revert the change in the 100th row from previous test
         trueFlags[100] = 1
         combinedZernikes, testFlags = self.task.combineZernikes(zernikeArray)
@@ -80,13 +80,33 @@ def testCombineZernikes(self):
         self.assertTrue(isinstance(testFlags[0], numbers.Integral))
 
         # Test that changing the maxZernClip parameter does change
-        # if a row is removed from the final result
+        # whether a row is removed from the final result
+        zernikeArray[50, 3:] += 100.0
+        zernikeArray[51, 3:] -= 100.0
         self.config.maxZernClip = 5
         self.task = CombineZernikesSigmaClipTask(config=self.config)
         combinedZernikes, testFlags = self.task.combineZernikes(zernikeArray)
         np.testing.assert_array_equal(np.ones(10) * 2.0, combinedZernikes)
         trueFlags[0] = 1
-        trueFlags[51] = 1
+        trueFlags[49:52] = 1
+        np.testing.assert_array_equal(trueFlags, testFlags)
+        self.assertTrue(isinstance(testFlags[0], numbers.Integral))
+
+    def testCombineZernikesEffectiveMaxZernClip(self):
+        testWhileZernikeArray = np.ones((3, 10))
+        testWhileZernikeArray[0, 4] = 3
+        testWhileZernikeArray[1, 3] = 3
+        testWhileZernikeArray[2, 2] = 3
+
+        # Test that changing the maxZernClip parameter does change
+        # whether a row is removed from the final result
+        self.config.maxZernClip = 6
+        self.task = CombineZernikesSigmaClipTask(config=self.config)
+        combinedZernikes, testFlags = self.task.combineZernikes(testWhileZernikeArray)
+        np.testing.assert_array_equal(testWhileZernikeArray[0], combinedZernikes)
+        self.assertEqual(self.task.metadata["maxZernClip"], 6)
+        self.assertEqual(self.task.metadata["effMaxZernClip"], 4)
+        trueFlags = np.array([0, 1, 1])
         np.testing.assert_array_equal(trueFlags, testFlags)
         self.assertTrue(isinstance(testFlags[0], numbers.Integral))