Talking to PTI over phone, Desai said he had sent his resignation to the Prime Minister Narendra Modi.
"I have tendered resignation on moral grounds after the formation of new government at the Centre, to give it the chance to appoint a new chairman," he said.
Earlier, Prime Minister Modi had invited Desai to Delhi, but the meeting was cancelled following death of Union Minister Gopinath Munde in a road accident.
"Unfortunately I could not meet the Prime Minister because of Munde's death, and then the Prime Minister could not spare time for another meeting," he said.