diff --git a/server/src/main/java/org/opensearch/repositories/RepositoriesService.java b/server/src/main/java/org/opensearch/repositories/RepositoriesService.java
index 07ff9239e255e..7da52147661dc 100644
--- a/server/src/main/java/org/opensearch/repositories/RepositoriesService.java
+++ b/server/src/main/java/org/opensearch/repositories/RepositoriesService.java
@@ -719,6 +719,16 @@ public static void validateRepositoryMetadataSettings(
                         + minVersionInCluster
                 );
             }
+            if (repositoryName.contains(SnapshotsService.SNAPSHOT_PINNED_TIMESTAMP_DELIMITER)) {
+                throw new RepositoryException(
+                    repositoryName,
+                    "setting "
+                        + SHALLOW_SNAPSHOT_V2.getKey()
+                        + " cannot be enabled for repository with "
+                        + SnapshotsService.SNAPSHOT_PINNED_TIMESTAMP_DELIMITER
+                        + " in the name as this delimiter is used to create pinning entity"
+                );
+            }
             if (repositoryWithShallowV2Exists(repositories)) {
                 throw new RepositoryException(
                     repositoryName,
@@ -766,17 +776,9 @@ private static boolean pinnedTimestampExistsWithDifferentRepository(
             settings,
             repositoriesService
         );
-        for (String pinningEntiy : pinningEntityTimestampMap.keySet()) {
-            String[] tokens = pinningEntiy.split(SnapshotsService.SNAPSHOT_PINNED_TIMESTAMP_DELIMITER);
-            if (tokens.length > 2) {
-                logger.warn(
-                    "With more than one {} in the pinning entity = {}, not able to determine if there is a pinned timestamp created with different repository",
-                    SnapshotsService.SNAPSHOT_PINNED_TIMESTAMP_DELIMITER,
-                    pinningEntiy
-                );
-                return true;
-            }
-            if (tokens[0].equals(newRepoName) == false) {
+        for (String pinningEntity : pinningEntityTimestampMap.keySet()) {
+            String repoNameWithPinnedTimestamps = pinningEntity.split(SnapshotsService.SNAPSHOT_PINNED_TIMESTAMP_DELIMITER)[0];
+            if (repoNameWithPinnedTimestamps.equals(newRepoName) == false) {
                 return true;
             }
         }
diff --git a/server/src/test/java/org/opensearch/repositories/blobstore/BlobStoreRepositoryRemoteIndexTests.java b/server/src/test/java/org/opensearch/repositories/blobstore/BlobStoreRepositoryRemoteIndexTests.java
index 3a81c616eda7f..e280ab8c7a73c 100644
--- a/server/src/test/java/org/opensearch/repositories/blobstore/BlobStoreRepositoryRemoteIndexTests.java
+++ b/server/src/test/java/org/opensearch/repositories/blobstore/BlobStoreRepositoryRemoteIndexTests.java
@@ -52,6 +52,7 @@
 import org.opensearch.repositories.fs.FsRepository;
 import org.opensearch.snapshots.SnapshotId;
 import org.opensearch.snapshots.SnapshotInfo;
+import org.opensearch.snapshots.SnapshotsService;
 import org.opensearch.test.OpenSearchIntegTestCase;
 
 import java.io.IOException;
@@ -391,6 +392,18 @@ public void testRepositoryCreationShallowV2() throws Exception {
             .put(SHALLOW_SNAPSHOT_V2.getKey(), true)
             .build();
 
+        String invalidRepoName = "test" + SnapshotsService.SNAPSHOT_PINNED_TIMESTAMP_DELIMITER + "repo-1";
+        try {
+            createRepository(client, invalidRepoName, snapshotRepoSettings1);
+        } catch (RepositoryException e) {
+            assertEquals(
+                "["
+                    + invalidRepoName
+                    + "] setting shallow_snapshot_v2 cannot be enabled for repository with __ in the name as this delimiter is used to create pinning entity",
+                e.getMessage()
+            );
+        }
+
         // Create repo with shallow snapshot V2 enabled
         createRepository(client, "test-repo-1", snapshotRepoSettings1);