The shadow foreign secretary said Mr Assad, who has presided over a civil war which has killed more than 450,000 people and displaced 11 million, may not be “as overwhelmingly unpopular as the rebels told the West”.
The Assad regime, which has been backed by Russia since 2015, has repeatedly been accused of using chemical weapons.
In an interview with the magazine Prospect, Ms Thornberry said: “There is an argument that if [President Assad] had been as overwhelmingly unpopular as the rebels told the West at the outset, then he wouldn’t be there.
“I think there has been a depth and a breadth of support for Assad that has been underestimated.”
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Elsewhere in the interview, Ms Thornberry said foreign forces, including Britain, which has struck Isis targets as well as the Syrian regime’s chemical weapons facilities, need to leave the country.
“They’re not fighting for the sake of the Syrian people,” she said.
She also suggested the UK should back peace talks overseen by Russia in Sochi. “I think we should be working with whatever works, for the sake of the Syrian kids. None of this is revolutionary,” she said.
Ms Thornberry refused to denounce Russia for vetoing 11 UN Security Council resolutions, saying: “People will always block resolutions. If you look at the number of resolutions America has blocked, I mean that’s the way of politics.”
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Her comments drew the ire of Kristyan Benedict, the UK campaigns manager for Amnesty International.
“Maybe @EmilyThornberry believes elections in Syria are ‘free & fair’ and believes the ludicrous numbers Assad gets,” he tweeted.
“Maybe she should talk to Syrian human rights activists who’ve had to escape Syria because they dared to call for genuine elections & democracy.”
In a later tweet, he said: “In Assad’s prison state, it’s a case of ‘love me or I’ll kill you’.”