In a video recorded January 5, 2016, and first obtained by the Cut, Matthews is seen preparing for the interview Clinton. "Precious waters?" Matthews was seemingly referring to Clinton.
The Cut obtained and published the video on Friday.
"This was a awful comment I made in poor taste during the height of the Bill Cosby headlines", Matthews said to the Cut "I realize that's no excuse".
Reps for Clinton didn't immediately respond to a request for comment from TheWrap.
Matthews' comment was in reference to allegations made by dozens of women against Bill Cosby, who said they were drugged and raped by the comedian, and is the latest in a series of allegations and questionable behavior surrounding the political commentator.
"As person who set up this interview and assured HRC & team I believed Chris would be fair, this makes me feel ill. Quit. Now", tweeted Tim Hogan, a former Clinton campaign spokesperson.
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MSNBC's Chris Matthews really stepped in it this time. Before embarking on a career in television, he cut his teeth on Capitol Hill, serving as an aide to former Speaker of the House Tip O'Neill.
The website also listed some of Matthews' controversial remarks about Clinton, some of which were made on air. He once pinched her cheek after an interview, and, in 2008 said, "the reason she's a US senator, the reason she's a candidate for president, the reason she may be a front-runner is her husband messed around". "She didn't win there on her merit".
"Did you see her walk?" "My God is that good".
The release of the footage comes as the nation reckons with sexual assault and harassment, with near-daily revelations about men falling from positions of power in entertainment, business, the media and politics.