The Rev. Ted Haggard also stepped aside as head of his 14,000-member New Life Church while a church panel investigates, saying he could "not continue to minister under the cloud created by the accusations."
The investigation came after a 49-year-old man told a Denver radio station that Haggard paid him to have sex.
Haggard, a married father of five, denied the allegations in an interview with KUSA-TV late Wednesday: "Never had a gay relationship with anybody, and I'm steady with my wife, I'm faithful to my wife."
In a written statement, Haggard said: "I am voluntarily stepping aside from leadership so that the overseer process can be allowed to proceed with integrity. I hope to be able to discuss this matter in more detail at a later date. In the interim, I will seek both spiritual advice and guidance."
Mike Jones, 49, told The Associated Press that Haggard paid him to have sex nearly every month for three years. His allegations were first aired on KHOW-AM in Denver.
Jones said that he had advertised himself as an escort on the Internet and that a man who called himself Art contacted him. Jones said he later saw the man on television identified as Haggard.
He said that he last had sex with Haggard in August and that he did not warn him before making his allegations this week.
Jones said he has voice mail messages from Haggard, as well as an envelope he said Haggard used to mail him cash, though he declined to make any of it available to the AP.
"There's some stuff on there (the voice mails) that's pretty damning," he said.
Richard Cizik, vice president for government affairs for the evangelicals association, expressed shock.
"Is this something I can imagine of Ted Haggard? No," he said.
Carolyn Haggard, spokeswoman for the New Life Church, said a four-member church panel will investigate the allegations. She did not identify the board members.
"This is really routine when any sort of situation like this arises, so we're prepared," she said. "The church is going to continue to serve and be welcoming to our community. That's a priority."