Around 30 protestors entered an auditorium at the LSE through a side door and chanted "minister for culture, Tory vulture" and "Tory scum".
Hunt was being interviewed at the university by broadcaster Raymond Snoddy.
The protestors quizzed Hunt over News Corp's bid to take full control of BSkyB.
Reports earlier in the week suggested that Hunt, who is responsible for the decision over the BSkyB takeover bid, was planning to meet with representatives from News Corp in private. Hunt refused to comment on the issue when asked by Snoddy prior to the protest.
One protestor asked Hunt whether he was a "free, fair and independent arbiter" in his decision over the bid "if he had held undocumented meetings with the son of Rupert Murdoch".
Amid shouting and boos from the event's audience, Hunt agreed to answer the question but said only: "The answer is yes, I am."
The protestors left the auditorium after about 15 minutes, urged on by LSE staff and Hunt's own security personnel.
The culture secretary was late to begin the interview after talking to some of the protestors outside the school. During the protest he agreed to speak with them again outside afterwards, but they had left the area by the time the event finished.
He told the LSE audience afterwards that: "While I'm sure that everyone here is annoyed by the interruption to the free speech and discussion taking place, I would rather live in a country where that was allowed to happen."
He later added: "They [the protestors] should realise that they interrupted a debate and made it more difficult to hold the government to account."
Hunt refused to comment on the decision making process over News Corp's bid for Sky during the interview, or when a decision will be made.
Video below from BBC College of Journalism: