diff --git a/server/src/main/java/org/elasticsearch/action/search/SearchResponseMerger.java b/server/src/main/java/org/elasticsearch/action/search/SearchResponseMerger.java
index 3b28ca19477..999ea9b2054 100644
--- a/server/src/main/java/org/elasticsearch/action/search/SearchResponseMerger.java
+++ b/server/src/main/java/org/elasticsearch/action/search/SearchResponseMerger.java
@@ -204,7 +204,25 @@ final class SearchResponseMerger {
             if (shardId2 == null) {
                 return 1;
             }
-            return shardId1.compareTo(shardId2);
+            int shardIdCompare = shardId1.compareTo(shardId2);
+            //we could assume that the same shard id cannot come back from multiple clusters as even with same index name and shard index,
+            //the index uuid does not match. But the same cluster can be registered multiple times with different aliases, in which case
+            //we may get failures from the same index, yet with a different cluster alias in their shard target.
+            if (shardIdCompare != 0) {
+                return shardIdCompare;
+            }
+            String clusterAlias1 = o1.shard() == null ? null : o1.shard().getClusterAlias();
+            String clusterAlias2 = o2.shard() == null ? null : o2.shard().getClusterAlias();
+            if (clusterAlias1 == null && clusterAlias2 == null) {
+                return 0;
+            }
+            if (clusterAlias1 == null) {
+                return -1;
+            }
+            if (clusterAlias2 == null) {
+                return 1;
+            }
+            return clusterAlias1.compareTo(clusterAlias2);
         }
 
         private ShardId extractShardId(ShardSearchFailure failure) {
diff --git a/server/src/test/java/org/elasticsearch/action/search/SearchResponseMergerTests.java b/server/src/test/java/org/elasticsearch/action/search/SearchResponseMergerTests.java
index 712d6a60440..c32ff7b88f8 100644
--- a/server/src/test/java/org/elasticsearch/action/search/SearchResponseMergerTests.java
+++ b/server/src/test/java/org/elasticsearch/action/search/SearchResponseMergerTests.java
@@ -109,7 +109,14 @@ public class SearchResponseMergerTests extends ESTestCase {
         SearchTimeProvider searchTimeProvider = new SearchTimeProvider(0, 0, () -> 0);
         SearchResponseMerger merger = new SearchResponseMerger(0, 0, SearchContext.TRACK_TOTAL_HITS_ACCURATE,
             searchTimeProvider, flag -> null);
-        PriorityQueue<Tuple<ShardId, ShardSearchFailure>> priorityQueue = new PriorityQueue<>(Comparator.comparing(Tuple::v1));
+        PriorityQueue<Tuple<SearchShardTarget, ShardSearchFailure>> priorityQueue = new PriorityQueue<>(Comparator.comparing(Tuple::v1,
+            (o1, o2) -> {
+                int compareTo = o1.getShardId().compareTo(o2.getShardId());
+                if (compareTo != 0) {
+                    return compareTo;
+                }
+                return o1.getClusterAlias().compareTo(o2.getClusterAlias());
+            }));
         int numIndices = numResponses * randomIntBetween(1, 3);
         Iterator<Map.Entry<String, Index[]>> indicesPerCluster = randomRealisticIndices(numIndices, numResponses).entrySet().iterator();
         for (int i = 0; i < numResponses; i++) {
@@ -120,15 +127,46 @@ public class SearchResponseMergerTests extends ESTestCase {
             ShardSearchFailure[] shardSearchFailures = new ShardSearchFailure[numFailures];
             for (int j = 0; j < numFailures; j++) {
                 ShardId shardId = new ShardId(randomFrom(indices), j);
-                ShardSearchFailure failure;
-                if (randomBoolean()) {
-                    SearchShardTarget searchShardTarget = new SearchShardTarget(randomAlphaOfLength(6), shardId, clusterAlias, null);
-                    failure = new ShardSearchFailure(new IllegalArgumentException(), searchShardTarget);
-                } else {
-                    ElasticsearchException elasticsearchException = new ElasticsearchException(new IllegalArgumentException());
-                    elasticsearchException.setShard(shardId);
-                    failure = new ShardSearchFailure(elasticsearchException);
-                }
+                SearchShardTarget searchShardTarget = new SearchShardTarget(randomAlphaOfLength(6), shardId, clusterAlias, null);
+                ShardSearchFailure failure = new ShardSearchFailure(new IllegalArgumentException(), searchShardTarget);
+                shardSearchFailures[j] = failure;
+                priorityQueue.add(Tuple.tuple(searchShardTarget, failure));
+            }
+            SearchResponse searchResponse = new SearchResponse(InternalSearchResponse.empty(), null,
+                1, 1, 0, 100L, shardSearchFailures, SearchResponse.Clusters.EMPTY);
+            addResponse(merger, searchResponse);
+        }
+        awaitResponsesAdded();
+        assertEquals(numResponses, merger.numResponses());
+        SearchResponse.Clusters clusters = SearchResponseTests.randomClusters();
+        SearchResponse mergedResponse = merger.getMergedResponse(clusters);
+        assertSame(clusters, mergedResponse.getClusters());
+        assertEquals(numResponses, mergedResponse.getTotalShards());
+        assertEquals(numResponses, mergedResponse.getSuccessfulShards());
+        assertEquals(0, mergedResponse.getSkippedShards());
+        assertEquals(priorityQueue.size(), mergedResponse.getFailedShards());
+        ShardSearchFailure[] shardFailures = mergedResponse.getShardFailures();
+        assertEquals(priorityQueue.size(), shardFailures.length);
+        for (ShardSearchFailure shardFailure : shardFailures) {
+            ShardSearchFailure expected = priorityQueue.poll().v2();
+            assertSame(expected, shardFailure);
+        }
+    }
+
+    public void testMergeShardFailuresNullShardTarget() throws InterruptedException {
+        SearchTimeProvider searchTimeProvider = new SearchTimeProvider(0, 0, () -> 0);
+        SearchResponseMerger merger = new SearchResponseMerger(0, 0, SearchContext.TRACK_TOTAL_HITS_ACCURATE,
+            searchTimeProvider, flag -> null);
+        PriorityQueue<Tuple<ShardId, ShardSearchFailure>> priorityQueue = new PriorityQueue<>(Comparator.comparing(Tuple::v1));
+        for (int i = 0; i < numResponses; i++) {
+            int numFailures = randomIntBetween(1, 10);
+            ShardSearchFailure[] shardSearchFailures = new ShardSearchFailure[numFailures];
+            for (int j = 0; j < numFailures; j++) {
+                String index = "index-" + i;
+                ShardId shardId = new ShardId(index, index + "-uuid", j);
+                ElasticsearchException elasticsearchException = new ElasticsearchException(new IllegalArgumentException());
+                elasticsearchException.setShard(shardId);
+                ShardSearchFailure failure = new ShardSearchFailure(elasticsearchException);
                 shardSearchFailures[j] = failure;
                 priorityQueue.add(Tuple.tuple(shardId, failure));
             }