The presenter said she “infuriated the prime minister” on the programme in 1990.
Wark told Radio Times magazine: “She didn’t like being interviewed by women and Downing Street tried to get me taken off the job (to do the interview).
“The BBC were steadfast. ‘There’s absolutely no question of that’, they said, ‘You’re not dictating who does the interview’. The same would be the case today.”
She added Mrs Thatcher did try to get her onside before the interview.
Wark said: “Margaret Thatcher didn’t talk much in make-up but she’d done her research because she tried to soften me up by saying, ‘It’s difficult for women holding down a career’.”
She said of the interview: “Mrs Thatcher thought I was impertinent, though I don’t think she would have thought a man was impertinent.
“I’d made her feel so uncomfortable that she had a very sharp go at me afterwards.
“She was standing right up beside me, accusing me of interrupting her. I just smiled, and stood my ground, I was polite.”
Wark also said Newsnight was offered behind-the-scenes access to Barack Obama, who had then been in the state senate and was little known in the UK, at the Democratic National Convention in 2004 “to make a film in the lead-up to the speech, but the powers that be didn’t want it”.
She added: “Now I think, ‘Good God! We’d have been so far ahead of the curve’, What a piece of history that would’ve been.”