diff --git a/x-pack/plugin/snapshot-repo-test-kit/src/internalClusterTest/java/org/elasticsearch/repositories/blobstore/testkit/integrity/RepositoryVerifyIntegrityIT.java b/x-pack/plugin/snapshot-repo-test-kit/src/internalClusterTest/java/org/elasticsearch/repositories/blobstore/testkit/integrity/RepositoryVerifyIntegrityIT.java
index 4b0e0fdbb0955..5725b065aeb06 100644
--- a/x-pack/plugin/snapshot-repo-test-kit/src/internalClusterTest/java/org/elasticsearch/repositories/blobstore/testkit/integrity/RepositoryVerifyIntegrityIT.java
+++ b/x-pack/plugin/snapshot-repo-test-kit/src/internalClusterTest/java/org/elasticsearch/repositories/blobstore/testkit/integrity/RepositoryVerifyIntegrityIT.java
@@ -344,16 +344,23 @@ public void testCorruption() throws IOException {
                 ? equalTo(testContext.indexNames().size())
                 : lessThan(testContext.indexNames().size())
         );
-        assertThat(anomalies, not(empty()));
+        // Missing shard generation file is automatically repaired based on the shard snapshot files.
+        // See also BlobStoreRepository#buildBlobStoreIndexShardSnapshots
+        final boolean deletedShardGen = corruptedFileType == RepositoryFileType.SHARD_GENERATION && Files.exists(corruptedFile) == false;
+        assertThat(anomalies, deletedShardGen ? empty() : not(empty()));
         assertThat(responseObjectPath.evaluate("results.total_anomalies"), greaterThanOrEqualTo(anomalies.size()));
-        assertEquals("fail", responseObjectPath.evaluate("results.result"));
+        assertEquals(deletedShardGen ? "pass" : "fail", responseObjectPath.evaluate("results.result"));
 
         // remove permitted/expected anomalies to verify that no unexpected ones were seen
         switch (corruptedFileType) {
             case SNAPSHOT_INFO -> anomalies.remove("failed to load snapshot info");
             case GLOBAL_METADATA -> anomalies.remove("failed to load global metadata");
             case INDEX_METADATA -> anomalies.remove("failed to load index metadata");
-            case SHARD_GENERATION -> anomalies.remove("failed to load shard generation");
+            case SHARD_GENERATION -> {
+                if (deletedShardGen == false) {
+                    anomalies.remove("failed to load shard generation");
+                }
+            }
             case SHARD_SNAPSHOT_INFO -> anomalies.remove("failed to load shard snapshot");
             case SHARD_DATA -> {
                 anomalies.remove("missing blob");