59-year-old Khanday, who served as Principal Secretary to Mufti Sayeed during his term as Chief Minister in 2002, sent his papers to the state Government for acceptance.
"I have sought voluntary retirement. I have submitted my papers yesterday," Khanday told PTI here today. He, however, refused to divulge the reasons for his action.
A 1978-batch IAS officer, Khanday was made Chief Secretary by the previous Omar Abdullah-led Government in February 2013. He was due to retire on November 30 this year.
Khanday had opposed recent bureaucratic reshuffle carried out by the state government and as a protest kept himself away from the cabinet meeting held on August 21.
His absence had raised speculation that he may put in his papers due to differences between him and the ruling PDP-BJP alliance.
Reacting to the development, Omar tweeted, "another sign that things in J&K aren't going as smoothly as some people would like to have us believe.