Rathgeber, who represents the Alberta riding of Edmonton-St. Albert, announced his resignation on Twitter late Wednesday.
He had complained last week about disappointment in the party base about scandals in the federal government.
The government appears disappointed with Rathgeber's decision.
PMO communications director Andrew MacDougall tweeted that voters in Rathgeber’s riding elected a Conservative and "he should resign and run in a by-election."
In his comments last week, Rathgeber said federal power had slowly been transferred from the House of Commons to the cabinet and ultimately to the Prime Minister's Office.
Rathgeber, who has a reputation for being blunt and straightforward, said the Conservatives were elected in part on a promise to change that.
In late March, Rathgeber rose in the Commons to support the idea of an unbridled right to speak about any subject without having it first vetted by a party whip.
``In a Parliament where the government and the opposition control such a large portion of the parliamentary calendar and agenda, private members' bills, motions, are the very few mechanisms that members have to bring matters of importance from their constituents forward,'' said Rathgeber.
``I would submit that if the House does not jealously protect the rights of the members to bring forward matters of concern to their constituents ... the role of the private member, and Parliament and ultimately democracy have all equally been compromised.''
His statement came after fellow Tory Mark Warawa appealed to his colleagues to allow his motion condemning sex-selective abortions.
In a tweet to Rathgeber late Wednesday, Warawa wrote, ”Brent, you are a man of integrity and will be missed."
Rathgeber, a native of Melville, Sask., is a two-time MP first elected in 2008.
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