Father Pat Conroy resigned on April 15 after spending almost seven years praying at the beginning of the sessions of the House.
He wrote two versions of his resignation letters, both obtained by CNN from a source in Congress.
In the first letter, he wrote "as you requested, I offer my resignation …" The second letter did not include being 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 indicated that his last day would be May 24.
Conroy did not immediately respond to CNN's request for comment.
Ryan spokeswoman AshLee Strong denied that Conroy was expelled for anything she said or did, but did not elaborate on what triggered the resignation request.
"The speaker consulted with the minority leader, but the decision was his," he said. CNN in a statement. "He continues to be grateful for Father Conroy's service."
An assistant to House minority leader Nancy Pelosi told CNN that she made it clear to Ryan that she had only received positive comments about Conroy's service from House legislators. The assistant also said that Pelosi made it clear to Ryan that he did not agree with his decision.
It is not immediately clear why Conroy was asked to resign. Democratic Rep. Gerry Connolly said he was not sure why Ryan made the decision and wants the Wisconsin Republican to answer questions about "this violation he created." Ryan and Connolly are Catholics.
"For many members, the outrage is personal, and it's not about Catholicism," Connolly told CNN. "It's about this relationship with this personal counselor, it's very personally offensive to many members."
A group of bipartisan members of the House, including Connolly, is drafting a letter to Ryan asking him to explain why he asked Conroy to resign.
"We are seeking additional information regarding your decision to request the resignation of the Rev. Patrick J. Conroy, the 60th Chaplain of the House of Representatives," the letter said, which was obtained by CNN. "The sensitive nature of this situation requires a description of the process followed to arrive at the decision and a justification for that decision."
Conroy was not afraid to influence political issues in the past. He had mentioned the Republican tax bill in a sentence on November 6, 2017, before the legislation became law.
Daniel Burke of CNN contributed to this report.