Official sources said Governor P B Acharya accepted Zeliang's resignation and told him to continue till further arrangements were made.
Earlier in the day, Zeliang announced his decision to step down.
A statement from the Chief Minister's Office confirmed Zeliang was stepping down and that a consensus leader will be chosen tomorrow morning at Naga People's Front Legislature Party meeting.
The NPF meeting will be followed by a meeting of DAN (Democratic Alliance of Nagaland) at 11 AM here.
More From This Section
NPF sources said both Rio and Zeliang met Union Home Minister Rajnath Singh in New Delhi yesterday but they refused to divulge details.
The BJP has four MLAs in the state.
Zeliang had left for Delhi on February 16 after seeking two days' time to step down from the chief ministerial post.
Protests had erupted in Nagaland after the state government announced that in the Urban Local Bodies (ULBs) election, 33 per cent of the seats would be reserved for women.
The Nagaland government had fulfilled the demand of Nagaland Tribes Action Committee (NTAC) Kohima and Joint Coordination Committee (JCC), declaring the entire process of Urban Local Bodies election with 33 per cent reservation for women as null and void.
Its second demand of suspending the personnel involved in January 31 police firing on the protesters leading to the killing of two youths in Dimapur has been partially fulfilled as they have been transferred.