Meghalaya Chief Minister JD Rymbai resigned on Saturday following directions from the Congress leadership.
"Rymbai has quit the post," Major Ved Prakash, the party secretary in charge of Meghalaya, told in New Delhi.
Although Congress President Sonia Gandhi had asked Rymbai to quit following internal squabbles in the state unit, the chief minister was defiant and said he was ready to face any consequence.
"The state unit of the party is seized of the matter. The party will be taking necessary measures to avoid a political crisis," Congress secretary Tom Vadakkan added.
The chief minister was asked to step down by Gandhi on Tuesday night during a meeting in New Delhi.
Rymbai was sworn in as chief minister on June 15, 2006, succeeding DD Lapang, in the wake of dissidence in the party.
Meghalaya has seen six different governments with varied combinations of political parties, resulting in four chief ministers in five years between 1998 and the last assembly elections in 2003.
There were just two occasions, since Meghalaya attained statehood in 1972, when a chief minister was able to complete the full five-year term.