Nayak also resigned from the post of the national general secretary of the party's Scheduled Tribe Morcha.
"I have resigned from the primary membership of BJP and also from the post of national general secretary of the party's ST Morcha," Nayak told reporters.
"I have resigned protesting the attitude of the senior leaders in the state BJP," he said.
However, after his meeting with BJD supremo and Chief Minister Naveen Patnaik a couple of days back, speculations are rife that he would soon join BJD.
Nayak, a prominent leader in the Mayurbhanj district, was a minister in the Naveen Patnaik's ministry from 2000 to 2009 until his party's alliance broke with BJD.
Terming Nayak's action as "betrayal", state BJP president K V Singhdeo said the leader's resignation would hardly affect the party's electoral prospect in the forthcoming Lok Sabha polls.
"He was given party ticket and made minister twice. It's wrong to say that the state leadership ignored him," Singhdeo said in a statement.
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