Gates pleaded guilty last month to lying to the FBI and conspiring to defraud the United States, and he has agreed to cooperate with Mueller's investigation into Russian meddling in the 2016 election and whether there was any collusion with Moscow by Trump's campaign.
Three sources say that Mueller's team is now looking at the possibility that Dowd made pardon offers to both former Trump advisers previous year because the president's team was concerned about what they might say if they struck a deal with the special counsel.
Manafort - who is fighting charges from Mueller that relate to his work prior to joining Trump - left the campaign in August 2016 after reports about questionable payments he received from his work related to Ukraine.
At the White House press briefing, Press Secretary Sarah Sanders responded to questions about the article by referring back to Cobb's statement.
But offering it as a possibility to someone who is the focus of a criminal investigation with the intention of limiting their possible co-operating with that investigation could be of interest to Mueller - and those around the president do not carry the same power of pardon as he does.
Dowd spoke about a pardon with Manafort's lawyer, Reginald Brown, before Manafort was indicted last October, according to the Times.
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Legal experts were split on whether such a discussion would amount to obstruction of justice, even if Dowd broached the idea with Trump before talking to lawyers for Manafort and Flynn - a point that the New York Times said remained unclear. He pleaded guilty earlier this year to lying to the Federal Bureau of Investigation about his interactions with Gates and the former intelligence officer and is to be sentenced on April 3.
Two weeks after Flynn's guilty plea, Trump was asked by reporters whether he would pardon the retired Army three-star general.
Hours later, Flynn's brother posted a new tweet saying, "Mr. President, I personally believe that a pardon is due to General Flynn, given the apparent and obvious illegitimacy of the manner in which the so called "crimes" he plead (sic) guilty to were extracted from him".
"We're very confident in that and look forward to this process wrapping up".
Dowd, who announced his resignation last week, denied the claims to the Times: "There were no discussions".
Van der Zwaan pleaded guilty last month to one count of making false statements to investigators in the Russian Federation investigation, which is examining the extent of Russia's interference in the 2016 election and whether members of the Trump campaign colluded with Moscow to sway the race in Trump's favor.