(CNN) -- A New York Times report that Sen. John McCain once had a close relationship with a female lobbyist was "highly implausible," a former McCain aide told CNN.
Sen. John McCain, with his wife, Cindy, at his side, said The New York Times report is "not true."
The newspaper first reported online Wednesday that aides to McCain's 2000 presidential campaign were so worried about a relationship between McCain and lobbyist Vicki Iseman that they confronted the two of them.
Some McCain advisers also were concerned that the relationship had become romantic, the Times reported.
Iseman represented telecommunications companies with business before the Senate Commerce Committee, which McCain then chaired.
Dan Schnur, McCain's communication director during his 2000 presidential bid, told CNN on Thursday that he was involved in most high-level situations and that such a problem almost certainly would have "landed on my desk."
Schnur said that he was unaware of any "improper" relationship between the senator and Iseman and that he had never heard of any meeting with staffers and McCain about such a concern.
Schnur, a professor of political science at the University of California-Berkeley, has no connection to the McCain camp now.
Schnur said he spoke on the record with a Times reporter in December and said he knew of no problems surrounding Iseman. He said he was surprised the paper gave no hint of his views.
Schnur acknowledged that he could not be 100 percent sure about the story, but he said he believes his close contact and access would have brought such a situation to his attention.
McCain said Thursday that he has never "done anything that would betray the public trust or make a decision" that would favor a particular group.
McCain said he never had discussions with any staffers about an inappropriate relationship with Iseman. He also denied having a romantic relationship with her. If staffers had such concerns, McCain told reporters, they never conveyed them to him.
In a statement Thursday, The New York Times said it stands by its reporting and that "the story speaks for itself."
"We publish stories when they are ready," Executive Editor Bill Keller said in a statement, explaining the article reached his desk Tuesday. " '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."
The Times article explored McCain's relationships with and stances toward lobbyists and special interests.
Gabriel Sherman of The New Republic magazine said Thursday that a disagreement between Keller and the reporters who wrote the article had held up its publication.
The magazine started asking about the Times article after a report appeared on the Drudge Report Web site earlier this month, Sherman said.
The New Republic on Thursday published an article on its Web site about the Times investigation after the newspaper's report appeared.
"We got a sense from Mr. Keller and the paper that they did not want this article, this back story, told about why they were holding the McCain investigation," Sherman said.
"The reporters felt they they had nailed the story. Bill Keller and the editors felt they needed more documentary proof in the absence of a photograph or hotel receipt that proved this alleged affair," Sherman said.
"The reporters felt they nailed it. The editors felt they needed more, and, eventually, the reporters' view won out."
McCain's former top political adviser, John Weaver, told the newspaper that he met with Iseman at Washington's Union Station during the 2000 presidential bid. He asked her to stay away from the senator, the paper reported, because McCain was running on a platform of political reform and shunning special interests.
"Ms. Iseman's involvement in the campaign, it was felt by us, could undermine that effort," Weaver told the Times.
In an interview Thursday with CNN, Weaver said he approached Iseman because she was telling people she had special access to and influence with McCain.
The Times article didn't say Weaver and Iseman discussed any romantic relationship, and Weaver told CNN they never talked about it because "there was no reason to."
"My concern wasn't about anything John had done; it was about her comments. It was about access she claimed to have had," Weaver said.
Weaver left the McCain camp last summer but said he still talks daily to the senator's campaign officials.
Iseman acknowledged the Union Station meeting but disputed Weaver's account, according to the Times.
"I never discussed with him alleged things I had 'told people,' that had made their way 'back to' him," Iseman told the newspaper in an e-mail. She added that she never received special treatment from McCain's office, according to the paper.
CNN has not been able to reach Iseman for comment.
One of McCain's senior advisers, Charlie Black, said that information and documents provided to the paper disputes suggestions McCain tried to use his influence to help Iseman. Watch Black address the allegations »
Black accused the Times of being a liberal newspaper that was printing "rumors and gossip," and he called the article a partisan attack on the conservative McCain.
The newspaper endorsed McCain as the GOP nominee in the 2008 presidential race. E-mail to a friend
CNN's Dana Bash and Scott Bronstein contributed to this report.