A Rashtrapati Bhawan communique issued late last night said that Sankaranarayanan has been shifted to Mizoram and Gujarat Governor OP Kohli has been asked to discharge his duties.
82-year-old Sankaranarayanan, a senior Congress leader, was among the first batch of governors who was telephoned by Home Secretary Anil Goswami to put in his papers after change of government at the Centre. His tenure ends in 2017.
After a nudge from the Home Secretary, Sankaranarayanan had said in June that he will consider quitting if asked by an "appropriate authority".
Sankarnaryana has been transferred to a post that was held by Kamla Beniwal who was sacked earlier this month.
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A month earlier Beniwal was posted to Mizoram from Gujarat where she had some run-in with then Chief Minister Narendra Modi. 87-year-old Beniwal was removed just two months before her tenure was due to end.
Sankaranarayanan has been serving as Governor of Maharashtra since 22 January, 2010. He took oath as Governor of Maharashtra for a second time on 7 May, 2012 after the President granted him a fresh term of 5 years.
The apex court had also issued notice to Goswami who had allegedly threatened Governor Aziz Qureshi to resign from the post or face removal by Centre.
Virendra Kataria, a former Congress leader, was also sacked as Puducherry Governor last month.
Goswami is believed to have telephoned some of the Governors, appointed by the previous UPA regime, asking them to step down after which West Bengal Governor M K Narayanan, Nagaland Governor Ashwani Kumar, UP Governor B L Joshi and Chhattisgarh Governor Shekhar Dutt put in their papers.