Graham Brady has been elected chairman of the Conservative backbench 1922 committee.
He won 126 votes to 85 for Richard Ottoway.
The result has been reported as a blow for David Cameron, who pushed through a rule change to the 1922 committee.
Traditionally MPs on the government payroll have been excluded from taking part in the committee's proceedings.
At a meeting held last week Conservative MPs backed the change 168 to 118.
Ministers and PPS' were now able to vote for the chairmanship, but the prime minister later backed down and said only backbenchers would vote.
Brady, MP for Altrincham and Sale West, has been critical of the Tory high command, and has said he would have preferred a minority Conservative government than the coalition with the Lib Dems.
He won the backing of grassroots website ConservativeHome.com.
Co-editor Tim Montgomerie said Brady is man of principle but not a troublemaker.
"David Cameron has an iron grip on most of the Conservative party," he said.
"Lifelong friends form the core of his Downing Street staff. Another lifelong friend is the new co-chairman of the party.
"We need an independent voice as chairman of the '22 but not someone who will be voicing every thought to the nation's newspapers and broadcasters."
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