After debugging further, it seems that hbase hbck is not working properly. It is taking up incorrect hbase rootdir. Excerpt from hbck output   2018-01-05 11:28:44,051 INFO [main] util.HBaseFsck: Loading region directories from HDFS ERROR: Version file does not exist in root dir hdfs://nameservice1/tmp/hbase-hbase/hbase 2018-01-05 11:28:44,162 INFO [main] util.HBaseFsck: Loading region information from HDFS The rootdir being picked up is /tmp/hbase-{user running hbck command}/hbase. I am not sure why hbck is checking there instead of defined rootdir '/hbase'. Maybe due to this any of the hbck options commands are not running. ... View more