The chief secretary of Jammu and Kashmir, Iqbal Khandey, submitted his resignation on Tuesday citing differences with the Mufti Mohammed Sayeed government.
In a letter written to the chief minister, Khandey, who has three months of service still left, asked to be relieved with immediate effect. He was due to retire in November this year.
Sources said Khandey wrote that he has no moral right to continue as "the government doesn't trust him."
The chief secretary was not consulted on major administrative decisions including transfer and posting of officers and had expressed his reservations at last week's cabinet meeting, sources said.
The second senior-most IAS officer in the state, BR Sharma, is likely to replace Khandey as the new chief secretary.
In his letter, Khandey asked the government to treat his pending three months of service as leave and allow him to take voluntary retirement.
He did not even attend the cabinet meeting on August 21 which started speculations on his future with the Sayeed government. Sources later clarified that the chief secretary could not attend because of a death in the family, and that his request for postponement was turned down.
An IAS officer from the 1978 batch, Khandey was made the chief secretary on February 18, 2013 when Omar Abdullah was heading the National Conference-Congress government in Jammu and Kashmir.
While no one from the government was available for comment, opposition National Conference called the development "unfortunate",
"It is very unfortunate that the current regime can choke an officer so much that he decides to quit," said NC Kashmir provincial president, Nasir Aslam Wani.