diff --git a/itests/src/test/resources/testconfiguration.properties b/itests/src/test/resources/testconfiguration.properties
index bfefc3b5f023..54e4d142b82a 100644
--- a/itests/src/test/resources/testconfiguration.properties
+++ b/itests/src/test/resources/testconfiguration.properties
@@ -368,7 +368,6 @@ llap.query.negative.files=\
   ctas_noperm_loc.q,\
   file_with_header_footer_negative.q,\
   msck_repair_5.q,\
-  msck_repair_6.q,\
   stack_trace.q,\
   table_nonprintable_negative.q,\
   udf_local_resource.q
diff --git a/ql/src/test/org/apache/hadoop/hive/ql/metadata/TestHiveMetaStoreChecker.java b/ql/src/test/org/apache/hadoop/hive/ql/metadata/TestHiveMetaStoreChecker.java
index a6188e1ad97e..2f316bec0d78 100644
--- a/ql/src/test/org/apache/hadoop/hive/ql/metadata/TestHiveMetaStoreChecker.java
+++ b/ql/src/test/org/apache/hadoop/hive/ql/metadata/TestHiveMetaStoreChecker.java
@@ -432,6 +432,30 @@ public void testPartitionsCheck() throws HiveException,
     System.err.println("Test completed - partition check");
   }
 
+  @Test
+  public void testPartitionUriMismatchCheck()
+      throws HiveException, IOException, TException, MetastoreException {
+    Table table = createTestTable(false);
+
+    List<Partition> partitions = hive.getPartitions(table);
+    Partition part = partitions.getFirst();
+
+    // Change location to inject "localhost" authority to simulate HDFS HA mismatch
+    String originalPathStr = part.getDataLocation().toString();
+    String manipulatedPathStr = originalPathStr.replace("file:/", "file://localhost/");
+
+    part.setLocation(manipulatedPathStr);
+    hive.alterPartition(catName, dbName, tableName, part, null, true);
+
+    CheckResult result = checker.checkMetastore(catName, dbName, tableName, null, null);
+
+    // MSCK should succeed and NOT report this partition as missing from FS or missing from DB
+    assertEquals(Collections.<String>emptySet(), result.getTablesNotInMs());
+    assertEquals(Collections.<String>emptySet(), result.getTablesNotOnFs());
+    assertEquals(Collections.<CheckResult.PartitionResult>emptySet(), result.getPartitionsNotOnFs());
+    assertEquals(Collections.<CheckResult.PartitionResult>emptySet(), result.getPartitionsNotInMs());
+  }
+
   @Test
   public void testDataDeletion() throws HiveException,
     IOException, TException {
diff --git a/ql/src/test/queries/clientnegative/msck_repair_6.q b/ql/src/test/queries/clientpositive/msck_repair_ignore_duplicate_dir.q
similarity index 100%
rename from ql/src/test/queries/clientnegative/msck_repair_6.q
rename to ql/src/test/queries/clientpositive/msck_repair_ignore_duplicate_dir.q
diff --git a/ql/src/test/results/clientnegative/msck_repair_6.q.out b/ql/src/test/results/clientpositive/llap/msck_repair_ignore_duplicate_dir.q.out
similarity index 71%
rename from ql/src/test/results/clientnegative/msck_repair_6.q.out
rename to ql/src/test/results/clientpositive/llap/msck_repair_ignore_duplicate_dir.q.out
index a6c22cc4779a..40dd8982f215 100644
--- a/ql/src/test/results/clientnegative/msck_repair_6.q.out
+++ b/ql/src/test/results/clientpositive/llap/msck_repair_ignore_duplicate_dir.q.out
@@ -29,4 +29,16 @@ Partitions not in metastore:	repairtable:p1=a
 PREHOOK: query: MSCK REPAIR TABLE default.repairtable
 PREHOOK: type: MSCK
 PREHOOK: Output: default@repairtable
-FAILED: Execution Error, return code 40000 from org.apache.hadoop.hive.ql.ddl.DDLTask. The partition 'repairtable:p1=a' already exists for tablerepairtable
+POSTHOOK: query: MSCK REPAIR TABLE default.repairtable
+POSTHOOK: type: MSCK
+POSTHOOK: Output: default@repairtable
+PREHOOK: query: DROP TABLE default.repairtable
+PREHOOK: type: DROPTABLE
+PREHOOK: Input: default@repairtable
+PREHOOK: Output: database:default
+PREHOOK: Output: default@repairtable
+POSTHOOK: query: DROP TABLE default.repairtable
+POSTHOOK: type: DROPTABLE
+POSTHOOK: Input: default@repairtable
+POSTHOOK: Output: database:default
+POSTHOOK: Output: default@repairtable
diff --git a/standalone-metastore/metastore-server/src/main/java/org/apache/hadoop/hive/metastore/HiveMetaStoreChecker.java b/standalone-metastore/metastore-server/src/main/java/org/apache/hadoop/hive/metastore/HiveMetaStoreChecker.java
index 11dc51b827ad..ccc604569712 100644
--- a/standalone-metastore/metastore-server/src/main/java/org/apache/hadoop/hive/metastore/HiveMetaStoreChecker.java
+++ b/standalone-metastore/metastore-server/src/main/java/org/apache/hadoop/hive/metastore/HiveMetaStoreChecker.java
@@ -457,13 +457,21 @@ void findUnknownPartitions(Table table, Set<Path> missingPartDirs,
       // will not return any results.
       pr.setPath(partPath);
 
-      // Check if partition already exists. No need to check for those partition which are present in db
-      // but no in fs as msck will override the partition location in db
+      /*
+       Check if partition already exists. No need to check for those partitions which are present in db
+       but not in fs as msck will override the partition location in db.
+       This edge case happens when a partition's URI in the metastore contains a port (e.g., :8020)
+       while the table's default FS does not (e.g., HA nameservice). The string mismatch causes
+       allPartDirs.remove() to fail, leaving the physical directory in the unknown list even though
+       it was successfully verified and added to correctPartitions. We can safely skip it.
+      */
       if (result.getCorrectPartitions().contains(pr)) {
-        String msg = "The partition '" + pr.toString() + "' already exists for table" + table.getTableName();
-        throw new MetastoreException(msg);
+        if (LOG.isDebugEnabled()) {
+          LOG.debug("The partition '{}' already exists in metastore for table {}", pr, table.getTableName());
+        }
+        continue;
       } else if (result.getPartitionsNotInMs().contains(pr)) {
-        String msg = "Found two paths for same partition '" + pr.toString() + "' for table " + table.getTableName();
+        String msg = "Found two paths for same partition '" + pr + "' for table " + table.getTableName();
         throw new MetastoreException(msg);
       }
       if (transactionalTable) {