With his wife, Cindy, standing by his side, John McCain lashed out Thursday at a report in The New York Times that hints at an improper relationship between the Republican presidential candidate relationship and a female lobbyist, and rebuked the paper for spreading false rumors.

The Times article cited campaign aides who said they tried to keep McCain and lobbyist Vicki Iseman apart during the 2000 election, fearing the two were giving the impression they were having an affair. It noted how McCain wrote to government regulators on behalf of a client of the lobbyist while he was chairman of the Senate Commerce Committee.

McCain called a press conference in Toledo, Ohio, to slam the paper for embellishing his committee activities on Iseman’s behalf.

“I’m very disappointed in The New York Times piece. It’s not true,” he said.

Asked about his relationship with the lobbyist, he said, “I have many friends in Washington who represent various interests and … I consider her a friend.”

He said he saw her “on occasion” at fundraisers, receptions and committee meetings, but that was all.

His wife Cindy defended her husband, saying, “He’s a man of great character and I’m very disappointed in The New York Times.”

The article, published in Thursday’s edition of the Times but released the day before on its Web site, rehashes rumors spread during McCain’s 2000 presidential campaign.

The lengthy profile carried four bylines and detailed instances where McCain seemed to contradict his own anti-special interest message. It described, for instance, how he flew on corporate jets of executives looking for his support. The article was framed by accounts of his alleged relationship with Iseman.

McCain, 71, and Iseman, 40, long ago denied ever having a romantic relationship, but the story argues that “his confidence in his own integrity has sometimes seemed to blind him to potentially embarrassing conflicts of interest.”

Times Executive Editor Bill Keller released a statement Thursday saying, “On the substance, we think the story speaks for itself.

“On the timing, our policy is, we publish stories when they are ready. ‘Ready’ means the facts have been nailed down to our satisfaction, the subjects have all been given a full and fair chance to respond, and the reporting has been written up with all the proper context and caveats. This story was no exception. It was a long time in the works. It reached my desk late Tuesday afternoon. After a final edit and a routine check by our lawyers, we published it,” he said.

The Arizona senator said his campaign had been repeatedly contacted by the newspaper about the story.

“For months The New York Times has submitted questions and we have answered them fully and exhaustively, and unfortunately many of those answers were not included in the rather long piece in The New York Times,” he said.

McCain lamented that “this whole story is based on anonymous sources,” saying that could encompass any of the more than 100 aides he’s had contact with through the Commerce Committee.

The newspaper quoted anonymous aides as saying they had urged McCain and Iseman to stay away from each other prior to his failed presidential campaign in 2000. In its own follow-up story, The Washington Post quoted longtime aide John Weaver, who split with McCain last year, as saying he met with lobbyist Iseman and urged her to steer clear of McCain.

Weaver told the Times he arranged the meeting before the 2000 campaign after “a discussion among the campaign leadership” about Iseman.

Speaking with FOX News, Weaver said he met with Iseman at Union Station in either 1999 or 2000, he can’t remember which year, for about five minutes. The nature of the conversation was not about romantic involvement, but instead about how she was going around telling people how much enormous influence she had on McCain.

As a campaign professional, he said he didn’t want anyone saying they had influence over McCain so he met with her and told her to quit boasting, especially since McCain was making lobbying legislation at the time. Weaver said the conversation with Iseman and other related topics were well vetted by The Boston Globe during the New Hampshire primary in 2000.

But McCain said he was unaware of any such conversation, and denied that his aides ever tried to talk to him about his interactions with Iseman.

“Since it was in The New York Times, I don’t take it at face value,” McCain said with a laugh.

Iseman’s firm Alcalde & Fay released a statement Thursday decrying the article’s contents as “malicious innuendo” that is “utterly false.”

“Alcalde & Fay’s relationship with Senator McCain has been professional, appropriate and consistent with his legislative, jurisdictional and constituent duties,” president Kevin Fay said in the statement. “The story is based upon the fantasies of a disgruntled former campaign employee and is without foundation or merit. Ms. Iseman is a hard working professional whose 18 year career has been exemplary and she has our full support. It is beneath the dignity of a quality newspaper to participate in such a campaign of character assassination.”

Rick Davis, McCain’s campaign manager in 2000, told FOX News on Thursday that the campaign never had deep concerns about the relationship with Iseman or allegations of illicit favors for her client.

“I never had a single instance where this was a major issue in our campaign or any kind of an issue. And the idea that a decade later they have somehow uncovered some kind of a mystery is ridiculous,” Davis said.

Campaign spokeswoman Jill Hazelbaker likened the report to a “kind of gutter politics.”

“There is nothing in this story to suggest that John McCain has ever violated the principles that have guided his career,” she said.

Davis said the newspaper “didn’t say that there was anything improper here. They just tried to imply it. They didn’t say he had done anything for this lobbyist or this lobbying firm but they tried to imply it. If they are going to go this kind of route, why don’t they tell us where they got the information?”

The Times had endorsed McCain and Democratic candidate Hillary Clinton prior to the Super Tuesday primaries in New York Feb. 5.

With McCain now the presumptive nominee of his party, he said Thursday he intends to put the Times story to rest and move forward with the campaign.

Rumors of the newspaper’s investigation first surfaced two months ago, and at the time, senior officials in the McCain campaign adamantly denied to FOX News any personal or professional wrongdoing. Officials also confirmed that McCain had hired Washington attorney Bob Bennett to prepare the campaign for the coming “smear.” Bennett continues to be on retainer at this time.

“If there’s one thing I am absolutely confident of, it’s that John McCain is an honest man,” Bennett told FOX News Wednesday night. “I think for The New York Times to dig this up just shows that John McCain’s public statement about this is correct. It’s a smear job.”

Asked about the article, Republican rival Mike Huckabee wouldn’t comment on the newspaper’s allegations, but said he knows McCain to “be a man of integrity.”

“He is a good and decent and honorable man,” Huckabee said.

When details of the newspaper’s investigation emerged in December, McCain said he was going to battle the rumors much more vigorously than he fought other claims made against him in 2000.

“We’re getting close to the primary,” McCain said in December before he emerged as the presumptive Republican presidential nominee. “These allegations are coming out at a very interesting time, and I have never, ever done a favor for any lobbyist or special interest group.”

McCain’s denials in December, including of the alleged affair, was in response to expectations that the Drudge Report was going to preempt the investigation before the newspaper actually reported it, campaign officials said.

Though Drudge did not print the story, campaign officials contend that the newspaper decided to go ahead and publish it now because The New Republic was planning a scathing critique of the newspaper for revealing the contents of its investigation.

McCain campaign officials said two weeks ago, they got a call from The New Republic asking for comment and information because it was planning a story on the newspaper’s investigation.

Officials argued The New York Times, buffeted by reporter scandals in recent years, is covering itself, publishing a deliberate smear under pressure from the magazine and because of sensitivity to its reputation caused by reporter Judith Miller, who investigated Iraq’s weapons of mass destruction program and was a key player in the subsequent CIA leak investigation involving Valerie Plame.

The McCain stories also allege that the Arizona senator wrote letters and pushed legislation involving television station ownership that would have benefited Iseman’s clients.

In late 1999, McCain twice wrote letters to the Federal Communications Commission on behalf of Florida-based Paxson Communications — which had paid Iseman as its lobbyist — urging quick consideration of a proposal to buy a television station license in Pittsburgh. At the time, Paxson’s chief executive, Lowell W. “Bud” Paxson, also was a major contributor to McCain’s 2000 presidential campaign.

McCain did not urge the FCC commissioners to approve the proposal, but he asked for speedy consideration of the deal, which was pending from two years earlier. In an unusual response, then-FCC Chairman William Kennard complained that McCain’s request “comes at a sensitive time in the deliberative process” and “could have procedural and substantive impacts on the commission’s deliberations and, thus, on the due process rights of the parties.”

McCain addressed the letters Thursday, saying: “I said I’m not telling you how to make a decision; I’m just telling you that you should move forward and make a decision on this issue. I believe that was appropriate.”

Click here to read The New York Times profile of John McCain.

Read The Washington Post report.

Click here to read the story behind the story in The New Republic.

FOX News’ Jim Angle and Carl Cameron and The Associated Press contributed to this report.