Father Pat Conroy resigned on April 15, after praying for nearly seven years at the beginning of the house meetings.
He wrote two versions of his resignation letters, both received by CNN from a congressional source.
In the first letter he wrote: "As you requested, I hereby offer my resignation …" The second letter did not state that he was asked to resign. The first letter also said that Ryan should consult with his chief of staff on a resignation date, but the second letter stated that his last day would be May 24th.
Conroy did not immediately respond to CNN's request for comment.
Ryan's Ashlee Strong denies that Conroy was rejected for everything he said or did, but she did not elaborate on what triggered the resignation.
"The speaker has consulted with the minority leader, but the decision was his," she told CNN in a statement. "He is still grateful for the service of Father Conroy."
An adviser to House Minority leader Nancy Pelosi told CNN that she made it clear to Ryan that she had received only positive comments about Conroy's services from members of parliament. The counselor also said Pelosi made it clear to Ryan that she did not agree with his decision.
It is not immediately clear why Conroy was asked to resign. Democrat Gerry Connolly said he was not sure why Ryan made the decision and wanted to ask the Wisconsin Republican, "because of this gap he created". Both Ryan and Connolly are Catholic.
"For many members, the indignation is personal, and it's not about Catholicism," Connolly told CNN. "It's about this relationship with this personal adviser, it's very offensive to many members personally."
A group of bipartisan members of the House, including Connolly, is working on a letter to Ryan explaining why he has asked Conroy to resign
"We are seeking additional information about your decision, the 60th chaplain's resignation of the House of Representatives, Reverend Patrick J. Conroy, "reads the letter received from CNN. "The sensitivity of this situation requires a description of the process to make the decision and to find a rationale for this decision."
Conroy was not afraid to consider political issues in the past. He had mentioned in a prayer on November 6, 201
Daniel Burke of CNN contributed to this report.