Precious waters?' asks Matthews at the top of the tape, putting on a posh accent as he is handed a bottle of water that had been set aisde for Clinton.
The Cut's Noreen Malone, who uncovered the footage, noted that Matthews "then laughs, delighted with the line" and staffers are seen reacting "with disbelief, clearly uncomfortable".
In a video recorded January 5, 2016, and first obtained by the Cut, Matthews is seen preparing for the interview Clinton.
A spokeswoman for MSNBC referred BuzzFeed News to a statement Matthews made to the Cut.
"This was a bad 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".
According to the footage posted online, Matthews references the Bill Cosby scandals while joking with his staff before Clinton's arrival.
Dozens of women have accused Cosby of drugging them with pills and raping them. He said, "I deeply regret it and I'm sorry".
A fast-talking political junkie, Matthews has served as the host of "Hardball", a fixture on MSNBC's programming lineup, since 1997.
Back in 2008, he also pinched Clinton's cheek after conducting an interview with her, saying afterwards that he was "not obsessed" with the former First Lady.
In May 2016, Matthews was caught on a live microphone making comments about Melania Trump during then-presidential candidate Donald Trump's primary victory speech in Indiana.
MSNBC said it made a separation-related payment to an assistant producer on "Hardball" after she made a sexual harassment claim in 1999.
The MSNBC spokesman said that they thoroughly reviewed the situation at the time and that Matthews received a formal reprimand.
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