Jammu and Kashmir Governor N N Vohra accepted the minister's resignation.
"On the advise of Omar Abdullah, Chief Minister, Governor N N Vohra has accepted the resignation of Sajad Ahmad Kitchloo, minister of state, from the state council of ministers with immediate effect," a spokesman of the Raj Bhavan said in a statement here.
Kitchloo had earlier submitted his resignation to Chief Minister Omar Abdullah pending the outcome of the judicial probe ordered by the state government.
"I am forwarding the same to the Governor with the recommendation that it be accepted," he added.
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BJP and some Congress leaders had demanded Kitchloo be removed from the ministry pending an impartial inquiry on his alleged role in the Kishtwar riots.
"I want the truth to come out...My conscience does not allow me to continue as a minister till probe ends. I am resigning so that my presence does not cast a shadow on an independent probe," Kitchloo said in a statement.
"My conscience is clear, my electorate in Kishtwar vouch for my secular credentials and I am deeply hurt that some people have stooped so low as to accuse me of something I have not done, only for petty political gains," he said.
Kitchloo, representative of National Conference from Kishtwar Assembly constituency, was inducted in the council of ministers in January this year.