"I feel badly for him," Trump said, describing Manafort's legal troubles as a "very sad situation."
Manafort was ordered Wednesday to serve an additional 43 months on federal conspiracy charges , bringing his total sentence between two federal courts to 7.5 years in twin cases stemming from special counsel Robert Mueller's Russia investigation.
US District Court Judge Amy Berman Jackson told Manafort that, despite his apologies to the courtroom, his lawyers' arguments about the absence of any charges directly linked to collusion in the 2016 election were "just one more thing that's inconsistent with the notion of any genuine acceptance of responsibility."
In a plea cut in September 2018, Manafort admitted to money laundering, tax fraud and illegal foreign lobbying connected to his years of lucrative work for Ukrainian politicians, as well as defrauding banks to supplement his income with cash through mortgages.
He pleaded guilty to two criminal charges: conspiracy against the US and conspiracy witness tampering, which he committed after his arrest.
Jackson also considered that he intentionally lied to investigators and under oath before a grand jury about his contact with a Russian associate during the 2016 campaign, breaking his plea agreement.
"I am sorry for what I've done," Manafort told the courtroom. "Let me be very clear, I accept the responsibility for the acts that caused me to be here today."
Manafort was then hit with new criminal charges in New York City not even an hour after learning his prison sentence for federal crimes.
The new case throws a curveball to growing chatter that the President could pardon him. If convicted for crimes in Manhattan, Trump would have no power to issue a pardon.
The Manhattan district attorney on Wednesday charged the former Trump campaign chairman with mortgage fraud, falsifying business records and conspiracy for a total of 16 counts, the prosecutor's office announced. The charges relate to mortgages he received on properties in the New York area.
Without commenting directly on the new charges, Trump lamented his former aide's situation.
"On a human basis, it's a sad thing," he said.
The President said he hasn't considered pardoning Manafort, but did not rule out the possibility in the future.
"I have not even given it a thought as of this moment," Trump said when questioned about his pardon intentions for his former campaign chairman.
"It's not something now that's on my mind," he said, reiterating he felt "badly" for his former aide.