US House of Representatives Speaker Paul Ryan forced out the Jesuit priest who had served as House chaplain since 2011, in an apparent partisan squabble, a new report said Thursday.

House Democrats believe the ouster of Rev. Patrick Conroy was “because Republicans thought he was aligned with Democrats,” a senior Democratic aide told The Hill.

Conroy’s letter of resignation, a copy of which was obtained by The Hill, said he was stepping down because of a request from the Wisconsin Republican, who is also a Catholic.

“As you have requested, I hereby offer my resignation as the 60th Chaplain of the United States House of Representatives,” the April 15 letter to Ryan said.

Four sources — two from each party — told the website that Conroy was told he had to retire or he would be canned.

In a prayer during deliberations on tax cuts last year, Conroy asked that lawmakers should be “fair to all Americans,” a new report said Thursday.

One Democratic lawmaker said Ryan objected to the prayer on the House floor that Republicans viewed as critical of the GOP tax cut bill.

Other sources said Ryan thought Conroy favored Democrats in the House, and cited the prayer and the priest’s invitation to a Muslim to offer a prayer before the chambers as the reasons behind the chaplain’s demise.

“Some of the more conservative evangelical Republicans didn’t like that the Father had invited a Muslim person to give the opening prayer,” a source said.

A senior GOP aide said Conroy’s exit “was not because of any particular prayer.”

House Minority Leader Nancy Pelosi of California brought up the forced resignation during the Democrats’ whip meeting in the Capitol Thursday morning.

Ashlee Strong, a spokesman for Ryan, said it was the speaker’s decision, but offered no explanation for the move, adding that Pelosi and her office “were fully read in and did not object.”

Pelosi’s office disputed that she didn’t object.

“Leader Pelosi was given advance notice by Speaker Ryan,” said a Pelosi spokesman, but she “also made it clear to Speaker Ryan that she disagreed with this decision.”

Ryan has appointed Reps. Mark Walker (R-N.C.) and Tim Walberg (R-Mich.), both former pastors, to lead the search effort to find a new chaplain for when Conroy leaves at the end of May.