WASHINGTON — While Attorney General William P. Barr asserted his independence from the White House this week, he has also been quietly intervening in a series of politically charged cases, including against Michael T. Flynn, President Trump’s former national security adviser, people familiar with the matter said on Friday.

Mr. Barr installed a phalanx of outside lawyers to re-examine national security cases with the possibility of overruling career prosecutors, a highly unusual move that could prompt more accusations of Justice Department politicization. The case against Mr. Flynn, who twice pleaded guilty to lying to the F.B.I. in the Russia investigation, is a cause célèbre for Mr. Trump and his supporters, who say the retired general was ensnared in a “deep state” plot against the president.

The disclosures came as Mr. Trump made clear on Friday that he believes he has free rein over the Justice Department and its cases, rejecting Mr. Barr’s public demand of a day earlier that the president stop commenting on such cases.

Citing Mr. Barr’s assertion in an interview on Thursday that Mr. Trump had never asked him to act in a criminal case, the president declared on Twitter: “This doesn’t mean that I do not have, as President, the legal right to do so, I do, but I have so far chosen not to!”