Dowd insisted today that he did not raise the idea of pardons with lawyers representing the two men.
"I had no such discussions with them," Dowd said in a phone interview. "We never talked about pardons. There was no reason to talk about pardons. No ma'am."
A spokesman for Manafort, Jason Maloni, also declined to comment.
Robert Kelner, a lawyer for Flynn, declined to comment.
Legal experts said prosecutors could view the dangle of a presidential pardon to people under investigation as a criminal effort to obstruct justice.
Raising such a possibility could be viewed as an incentive for witnesses not to cooperate with investigators.
What Dowd precisely offered - and whether Trump was involved - could now become part of Mueller's investigation, which has included examining whether the President has taken steps to obstruct or stop the probe.
Legal experts are split about whether the President can commit obstruction of justice while exercising powers that are constitutionally afforded to him, like the pardon power.
"It's an open question about which there's been a great deal of debate," said Paul Rosenzweig, a lawyer who served on the team of Independent Counsel Ken Starr that investigated President Bill Clinton.
The full truth is that it's stone cold stupidity on his part if he actually did it
But, he added, "given the openness of both the legal and factual questions, it would be irresponsible of Mueller not to add this his inquiry."
"The full truth is that it's stone cold stupidity on his part if he actually did it," Rosenzweig added.
The New York Times first reported Dowd floated the idea of pardons with lawyers for Manafort and Flynn.
Flynn's family and advocates have indicated publicly that they are hoping Trump will pardon Flynn.
In December, after Flynn pleaded guilty, Trump was asked by reporters if he would be willing to pardon Flynn and Trump replied he wasn't ready to discuss it - "yet."
"We'll see what happens," he told reporters before a speech he was giving at the FBI's National Academy. "Let's see, I can say this: When you look at what's gone on with the FBI and the Justice Department, people are very, very angry."
The possibility of a pardon raises new questions about why Manafort has repeatedly refused to cooperate with Mueller's team. He faces a raft of serious charges, and if convicted, faces decades in prison.
