"The Governor acted unconstitutionally and in a partisan manner. Instead of regarding the advice of the council of ministers, he followed the advice of Congress. It is very unfortunate," Roy, who won a controversial trust vote yesterday, said.
Alleging the Shillong Raj Bhavan has turned into a 'Congress Bhavan', Roy said the cabinet adopted a resolution during the day expressing displeasure at the Governor's action.
The Meghalaya Progressive Alliance headed by Roy would lodge a protest with the President, Prime Minister and the Leader of Opposition in Lok Sabha, he said.
"Yesterday the assembly had voted for the government. The council of ministers has the mandate of the House. Why did the Centre impose President's Rule when we have elected representatives?" Roy said after a cabinet meeting.
"We are confused. What convinced the Governor to recommend President's Rule saying there was a constitutional breakdown? We will fight against it," he said, referring to a MPA decision to move the Supreme Court.
He also charged Congress with creating political instability and encouraging defection.