The senior Labour MP said he was embarrassed at the “rude and inappropriate” behaviour when Kuenssberg was doing her job.
Kuenssberg was invited to ask a question after Corbyn’s speech but was briefly prevented from speaking by hissing and boos from people in the crowd.
Corbyn was making a pro-EU speech on workers’ rights at the Institution of Engineering and Technology. He paused for several seconds as Kuenssberg prepared to ask her question, before putting up his hand to shush and quieten the crowd.
The BBC political editor has come under repeated attack from Corbyn supporters who accuse her of holding anti-Labour views.
The campaign group 38 Degrees hosted a petition calling for her to be sacked that attracted more than 35,000 signatures but later took it down, saying it had become a focal point for sexist abuse on social media.
Watson made his views about the incident clear on Twitter, saying: “Hissing is not the answer and it undermined Jeremy’s message.”
He added: “I understand people hold many views on how she does her job but ... hissing at her because of those views is wrong.”
Throughout the evening, he was bombarded by Twitter users defending the right of the audience to show their upset at Kuenssberg through hissing and booing.
Watson replied to many of them, sometimes sarcastically, telling one person: “Oh yes I can see it now, the hissing revolution. I think you might be onto something there. Please write it all up in a pamphlet.”
Clashes with what Corbyn’s supporters regard as an unsympathetic “mainstream media” have been a regular feature of his leadership.
Journalists said the atmosphere in the room after the speech was hostile. The Financial Times journalist Jim Pickard said the reaction was “pathetic”. Kuenssberg said: “Corbyn himself also mentioned importance of free press in his speech ... just saying.”
When the Labour leader was asked a question about whether he was getting his message across on the EU, he replied that was up to how the media covered it – and his supporters cheered, turning around to the journalists seated in one corner of the room.
During the row over the petition about Kuenssberg, Corbyn faced calls to condemn the targeting of the BBC political editor. The former Independent on Sunday political editor Jane Merrick said there was “a core of hard-left misogyny that comes out against women when Corbyn is under pressure – such as the abuse against [Labour MPs] Stella Creasy and Jess Phillips”.
At the time, the Labour leader distanced himself from those calling for Kuenssberg to be sacked. His spokesman said then: “Jeremy Corbyn is consistently on the record calling on people to treat each other with respect.”
A party spokesman later said: “Labour is committed to freedom of the press, freedom of speech and encourages everyone to treat people and opinions with respect.”
A senior party source said: “We don’t think it’s appropriate for journalists to be booed and jeered while they’re doing their job.”
This article was written by Rowena Mason and Jessica Elgot, for theguardian.com on Friday 3rd June 2016 09.15 Europe/Londonguardian.co.uk © Guardian News and Media Limited 2010