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“Padre, you just got to stay out of politics,” he recalled the speaker saying.

After his reinstatement, the chaplain chuckled over the controversy: “The upside of the whole story is people are actually reading my prayers,” he said.

But the dismissal itself hints at politics. Father Conroy is a Jesuit, an order of priests viewed by some as more liberal. The hubbub around Father Conroy is all the more contentious in Catholic circles because Mr. Ryan is a Catholic conservative.

Mr. Ryan’s move also exposed long-simmering tensions between Catholics and evangelicals in the House. After Father Conroy was forced out, Representative Mark Walker, Republican of South Carolina and a Southern Baptist minister, suggested that the next chaplain should be a family man — a remark that caused upset among Catholic because it implied that Catholic priests, who take a vow of celibacy, would not be eligible.

Mr. Walker later removed himself from a committee looking for a replacement for Father Conroy.

Father James Martin, a Jesuit priest and editor at large of America magazine, said it was “only just” that Father Conroy rescinded his resignation.

“Father Conroy’s firing was unjust, apparently motivated by no little anti-Catholicism, as his new letter indicates,” Father Martin said. “Speaker Ryan should have known that Jesuits have never been pushovers, especially when justice is at stake.”

In his letter to Mr. Ryan, Father Conroy took issue with Mr. Ryan’s apparent assertion that there were complaints about his pastoral care.

“This is not the reason that Mr. Burks gave me when asking for my ‘resignation,’ ” he wrote. “In fact, no such criticism has ever been leveled at me during my tenure as House chaplain. At the very least, if it were, I could have attempted to correct such ‘faults.’ In retracting my resignation I wish to do just that.”