Separately, a top McCain aide met with Ms. Iseman at Union Station in Washington to ask her to stay away from the senator. John Weaver, a former top strategist and now an informal campaign adviser, said in an e-mail message that he arranged the meeting after "a discussion among the campaign leadership" about her.
"Our political messaging during that time period centered around taking on the special interests and placing the nation’s interests before either personal or special interest," Mr. Weaver continued. "Ms. Iseman’s involvement in the campaign, it was felt by us, could undermine that effort."
Mr. Weaver added that the brief conversation was only about "her conduct and what she allegedly had told people, which made its way back to us." He declined to elaborate.
It is not clear what effect the warnings had; the associates said their concerns receded in the heat of the campaign.
Ms. Iseman acknowledged meeting with Mr. Weaver, but disputed his account.
"I never discussed with him alleged things I had ‘told people,’ that had made their way ‘back to’ him," she wrote in an e-mail message. She said she never received special treatment from Mr. McCain’s office.
Mr. McCain said that the relationship was not romantic and that he never showed favoritism to Ms. Iseman or her clients. "I have never betrayed the public trust by doing anything like that," he said. He made the statements in a call to Bill Keller, the executive editor of The New York Times, to complain about the paper’s inquiries.
The senator declined repeated interview requests, beginning in December. He also would not comment about the assertions that he had been confronted about Ms. Iseman, Mr. Black said Wednesday.
Mr. Davis and Mark Salter, Mr. McCain’s top strategists in both of his presidential campaigns, disputed accounts from the former associates and aides and said they did not discuss Ms. Iseman with the senator or colleagues.
"I never had any good reason to think that the relationship was anything other than professional, a friendly professional relationship," Mr. Salter said in an interview.
He and Mr. Davis also said Mr. McCain had frequently denied requests from Ms. Iseman and the companies she represented. In 2006, Mr. McCain sought to break up cable subscription packages, which some of her clients opposed. And his proposals for satellite distribution of local television programs fell short of her clients’ hopes.
The McCain aides said the senator sided with Ms. Iseman’s clients only when their positions hewed to his principles.
A champion of deregulation, Mr. McCain wrote letters in 1998 and 1999 to the Federal Communications Commission urging it to uphold marketing agreements allowing a television company to control two stations in the same city, a crucial issue for Glencairn Ltd., one of Ms. Iseman’s clients. He introduced a bill to create tax incentives for minority ownership of stations; Ms. Iseman represented several businesses seeking such a program. And he twice tried to advance legislation that would permit a company to control television stations in overlapping markets, an important issue for Paxson.
In late 1999, Ms. Iseman asked Mr. McCain’s staff to send a letter to the commission to help Paxson, now Ion Media Networks, on another matter. Mr. Paxson was impatient for F.C.C. approval of a television deal, and Ms. Iseman acknowledged in an e-mail message to The Times that she had sent to Mr. McCain’s staff information for drafting a letter urging a swift decision.
Mr. McCain complied. He sent two letters to the commission, drawing a rare rebuke for interference from its chairman. In an embarrassing turn for the campaign, news reports invoked the Keating scandal, once again raising questions about intervening for a patron.
Mr. McCain’s aides released all of his letters to the F.C.C. to dispel accusations of favoritism, and aides said the campaign had properly accounted for four trips on the Paxson plane. But the campaign did not report the flight with Ms. Iseman. Mr. McCain’s advisers say he was not required to disclose the flight, but ethics lawyers dispute that.
Recalling the Paxson episode in his memoir, Mr. McCain said he was merely trying to push along a slow-moving bureaucracy, but added that he was not surprised by the criticism given his history.
"Any hint that I might have acted to reward a supporter," he wrote, "would be taken as an egregious act of hypocrisy."
Statement by McCain
Mr. McCain’s presidential campaign issued the following statement Wednesday night:
"It is a shame that The New York Times has lowered its standards to engage in a hit-and-run smear campaign. John McCain has a 24-year record of serving our country with honor and integrity. He has never violated the public trust, never done favors for special interests or lobbyists, and he will not allow a smear campaign to distract from the issues at stake in this election.
"Americans are sick and tired of this kind of gutter politics, and there is nothing in this story to suggest that John McCain has ever violated the principles that have guided his career."