Khan was set to begin a speech on gender equality at the left-leaning think tank the Fabian Society when a group called the White Pendragons called for Khan's arrest as well as shouting pro-Trump and Brexit slogans.
The mayor and U.S. president have clashed publicly a number of times over issues like counter terrorism and Mr Trump's proposed state visit to the UK.
He then accused the Fabian Society of "subverting" the constitution.
The President to open the new United States embassy in south London and described the decision to move the building from Mayfair to Vauxhall as a "bad deal".
Donald Trump has "got the message" that many Londoners are staunchly opposed to his policies and actions, mayor Sadiq Khan said after the U.S. president cancelled his planned visit.
Mr Khan the visit would have been hampered by "mass peaceful protests" as Mr Trump's controversial views were the "polar opposite" of the city's values.
The men - who got into the event by buying tickets - also vowed to take the panel's chair Kate Green MP into custody as well as Sir Keir Starmer and general secretary Andrew Harrop.
One man could be heard addressing the audience with: "Ladies and gentlemen, we're here today to make a non-violent, peaceful citizen's arrest".
Security forces tried to eject the disrupters however they refused and said, "if you touch us, you'll be done for common assault. We're not leaving, we've paid for a ticket", reported the Evening Standard newspaper. Please stand back, do not touch us.
One of the protesters named Dave Russell, a self-described talk show host from London, live-streamed the protest to his Facebook account racking up thousands of views. Khan was able to continue his speech after the police forced the protesters out of the conference hall.
And in a dig at the USA president's recent Twitter meltdown, he said: 'It is a pleasure to be here even though we were distracted by the actions of what some would call very stable geniuses'.
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