"The Commission has removed him on a complaint from the Meghalaya government," Election Commissioner H.S. Brahma told IANS.
The transfer was necessary to ensure free and fair elections in state, he added.
Krishan was replaced with Prem Singh, a 1977-batch IPS officer of Assam-Meghalaya cadre, with immediate effect, a Meghalaya police official said.
Krishan has been appointed as director general of prisons, with additional charge of civil defence and home guards.
Meanwhile, four nomination papers out of the total of 355, including of 24 women candidates, were rejected during scrutiny of the forms Thursday.
The last date for withdrawal of candidature is Feb 8.