The meeting -- coming right before the FBI was set to announce the findings of its investigation into Hillary Clinton's private email server -- would eventually cast doubt on the Justice Department's impartiality in the matter, as the FBI is an agency of the DOJ.
"I do regret sitting down and having a conversation with him, because it did give people concern," she told CNN's Jake Tapper in an interview that aired Sunday on "State of the Union." "And as I said, my greatest concern has always been making sure that people understand that the Department of Justice works in a way that is independent and looks at everybody equally."
"And when you do something that gives people a reason to think differently, that's a problem," Lynch added. "It was a problem for me. It was painful for me, and so I felt it was important to clarify it as quickly and as clearly and as cleanly as possible."
In June, Lynch and Clinton met privately in Phoenix
after the former president realized he was on the same tarmac as the attorney general. The encounter became a major issue in the campaign considering it took place days before FBI Director James Comey announced that he would not press charges against Hillary Clinton over the server.
"I wish I had seen around that corner and not had that discussion with the former president, as innocuous as it was, because it did give people concern," Lynch said. "It did make people wonder is it going to affect the investigation that's going on, and that's not something that was an unreasonable question for anyone to ask."
Lynch originally told journalists at a press conference that in addition to discussing golf and grandchildren, she and the former president talked about "current news of the day, the Brexit decision and what it would mean."
"Brexit was the news of the day. There had just been a vote there," she told Tapper. "And as I indicated, we were told that President Clinton just wanted to say hello."
The conversation lasted about 45 minutes, which Lynch said was longer than she expected.
"It was just going to be hello, how are you, and everyone was going to go on about their evening, as far as we were concerned," she said.
But Lynch insists that there was nothing inappropriate about her time with Clinton.
"It was a very cordial discussion, as I said. Didn't have anything to do with the investigation or how it was going to be resolved, and in fact, we resolved it in the way that we discussed," she said.
Lynch also discussed Comey's decision to notify Congress it was reviewing emails that could have been pertinent to the FBI's investigation of her personal server. Many in the Clinton campaign believe the FBI's decision, coming less than two weeks before the election, swung the momentum to Donald Trump.
"People are very close to this issue right now, and certainly the Clinton campaign is going to be closer than anyone to this issue, so they're going to have strong feelings and strong views about that," Lynch said. "As I said, you know I allow people to have those feelings and to express them as they choose. That's their right."
But Lynch rejects the idea that her department handled the situation inappropriately.
"What we've said here is that you know we've handled the investigation in a way that was consistent with the way all investigations were handled. Unusual circumstances developed," she said. "The FBI director has spoken about why he made a decision to go in a particular route and how he made that decision. So I'm going to let that stand as it is."
Although Comey decided to deliver the letter to Congress, Lynch made it clear that she was not supportive of the idea and said it was one of a host of factors that may have influenced the results of the 2016 election. At the time, law enforcement officials told CNN that Lynch and her deputy, Sally Yates, disagreed with Comey's decision
to notify Congress, but that fallout over Bill Clinton's meeting with Lynch tied their hands.
"Discussions were had at the highest levels of the department. My views were made known, they were communicated to him," Lynch told Tapper.
"I think we're all going to be looking at that for a long time," she added.