"I think that it all bears a lot of reinvestigation," said McFarland, who served as Flynn's White House deputy before his firing by President Trump in February 2017.
"Not just what happened to General Flynn but the entire [thing]. It's time to investigate the investigators," she added.
"I know from my personal experience it was a very difficult, pressured time and you as an individual who's come at by the Justice Department, in my case the Mueller commission — you're an individual and you've got the entire weight of the United States government," McFarland continued. "They are in the position to really kind of do what they want."
She said the government should always have a powerful arsenal, but claimed they didn't need to bring down that sort of heat on people who were non-violent, and posed no physical threat.
"That's great if they are looking after terrorists and convicted criminals and hardcore people. You want them to have that ability," she said.
"But when it is used for a political purpose that's one of the most powerful instruments the United States government has. And to turn it for political purposes... We're going into very dangerous waters."
McFarland also said it's possible that Flynn's FBI interview memos, or 302s as they're called, were altered after the fact to pressure him into cooperating with the federal government. She also noted that one of the lead interviewers was later dismissed from the Bureau for bias.
"General Flynn did not have a lawyer with him when the two FBI Agents came to the White House," she said. "Now, when those interviews are finished the FBI Agents... take the handwritten notes and they file it in a digital file... They're not supposed to be tampered with, they're not supposed to be changed -- they're certainly not supposed to be changed after the fact."
"You have to trust the FBI to have done it accurately in an unbiased way," McFarland added. "The man who was his lead interviewer, who did the 302s, is someone who was later dismissed for bias."
Prosecutors have vigorously denied the claims lodged by Flynn's attorneys.