MSCK REPAIR TABLE throws null pointer exception

MSCK REPAIR TABLE statement throws null pointer exception in Hive 2.1
I have tested the same against external/internal tables created both in HDFS and in Google Cloud.

The error shown in beeline/sql client
Error: Error while processing statement: FAILED: Execution Error, return code 1 from org.apache.hadoop.hive.ql.exec.DDLTask (state=08S01,code=1)

Hive Logs:

2016-09-20T17:28:00,717 ERROR [HiveServer2-Background-Pool: Thread-92]: metadata.HiveMetaStoreChecker ()) - java.lang.NullPointerException
2016-09-20T17:28:00,717 WARN [HiveServer2-Background-Pool: Thread-92]: exec.DDLTask ()) - Failed to run metacheck:
org.apache.hadoop.hive.ql.metadata.HiveException: java.lang.NullPointerException
at org.apache.hadoop.hive.ql.metadata.HiveMetaStoreChecker.getAllLeafDirs(HiveMetaStoreChecker.java:444)
at org.apache.hadoop.hive.ql.metadata.HiveMetaStoreChecker.getAllLeafDirs(HiveMetaStoreChecker.java:388)
at org.apache.hadoop.hive.ql.metadata.HiveMetaStoreChecker.findUnknownPartitions(HiveMetaStoreChecker.java:309)
at org.apache.hadoop.hive.ql.metadata.HiveMetaStoreChecker.checkTable(HiveMetaStoreChecker.java:285)
at org.apache.hadoop.hive.ql.metadata.HiveMetaStoreChecker.checkTable(HiveMetaStoreChecker.java:230)
at org.apache.hadoop.hive.ql.metadata.HiveMetaStoreChecker.checkMetastore(HiveMetaStoreChecker.java:109)
at org.apache.hadoop.hive.ql.exec.DDLTask.msck(DDLTask.java:1814)
at org.apache.hadoop.hive.ql.exec.DDLTask.execute(DDLTask.java:403)
at org.apache.hadoop.hive.ql.exec.Task.executeTask(Task.java:197)
at org.apache.hadoop.hive.ql.exec.TaskRunner.runSequential(TaskRunner.java:100)
at org.apache.hadoop.hive.ql.Driver.launchTask(Driver.java:1858)
at org.apache.hadoop.hive.ql.Driver.execute(Driver.java:1562)
at org.apache.hadoop.hive.ql.Driver.runInternal(Driver.java:1313)
at org.apache.hadoop.hive.ql.Driver.run(Driver.java:1084)
at org.apache.hadoop.hive.ql.Driver.run(Driver.java:1077)
at org.apache.hive.service.cli.operation.SQLOperation.runQuery(SQLOperation.java:235)
at org.apache.hive.service.cli.operation.SQLOperation.access$300(SQLOperation.java:90)
at org.apache.hive.service.cli.operation.SQLOperation$2$1.run(SQLOperation.java:299)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:422)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1657)
at org.apache.hive.service.cli.operation.SQLOperation$2.run(SQLOperation.java:312)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.NullPointerException
at java.util.concurrent.ConcurrentHashMap.putVal(ConcurrentHashMap.java:1011)
at java.util.concurrent.ConcurrentHashMap.put(ConcurrentHashMap.java:1006)
at org.apache.hadoop.hive.ql.metadata.HiveMetaStoreChecker$1.call(HiveMetaStoreChecker.java:432)
at org.apache.hadoop.hive.ql.metadata.HiveMetaStoreChecker$1.call(HiveMetaStoreChecker.java:418)
... 4 more

Here are the steps to recreate this issue:
use default;
DROP TABLE IF EXISTS repairtable;
CREATE TABLE repairtable(col STRING) PARTITIONED BY (p1 STRING, p2 STRING);
MSCK REPAIR TABLE default.repairtable;