Prime Minister Manmohan Singh late on Friday evening asked Union Coal Minister Shibu Soren to resign from the council of ministers.
Soren, against whom an arrest warrant has been issued by a Jharkhand court in a 30-year-old murder case, has been untraceable for the last four days now.
Soren is an accused in the Chirudih massacre of 1975 in which 10 people were killed.
The prime minister's letter asking the minister to put in his papers was delivered to the latter's personal assistant in New Delhi.
Pressure was mounting on the United Progressive Alliance government to drop Soren with the Opposition stalling Parliamentary proceedings for the third consecutive day on Friday.
A Union minister hiding from the police is unprecedented and Soren had become a huge embarrassment for the government.