Coal Minister and Jharkhand Mukti Morcha chief Shibu Soren, against whom an arrest warrant has been issued by a Jharkhand court in a murder case, resigned from the Union council of ministers on Saturday.
The resignation has been accepted by President A P J Abdul Kalam.
Soren is an accused in the Chirrudih massacre of 1975, in which 10 people were killed.
Late on Saturday evening the prime minister had sent a letter to Soren's personal staff in New Delhi seeking the minister's resignation.
Party sources in Ranchi, earlier in the day, had indicated that Soren may wait till Monday, when his bail application will be heard in the high court, before deciding whether to step down.
The resignation was handed over to the prime minister at his residence by a JMM delegation in the afternoon.
The delegation comprised members of Parliament Tek Lal Mahato, Sudhan Marandi and Hemant Soren.
They were accompanied by Parliamentary Affairs Minister Ghulam Nabi Azad.