He also quit the post of Advisor to the Chief Minister for Mechanical Engineering with cabinet status.
Yhoshu's resignation letters have been sent to state Assembly, Chief Minister's Office and the NPF, copies of which have been sent to the media.
It is not immediately known whether he would join another party.
His resignation followed that of former home minister Y Patton on January 9. Patton has joined the BJP.
Election to the 60-member Nagaland Assembly will be held on February 27.
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