Boris Johnson has suffered a second major Tory rebellion over blocking post-Brexit free trade deals with countries that have committed genocide.

Furious Tory rebels blasted the government for “demeaning democracy” for denying them a straight vote on the so-called “genocide amendment” through “cynical manipulation” of Commons procedure.

The amendment would have given MPs the power to block trade deals with any country that the High Court rules is committing genocide, and is backed by dozens of Tories amid reports of abuses being carried out against Uighur Muslims in China’s Xinjiang province.

But the government denied the rebels a vote on the proposals by instead throwing its backing behind a rival amendment from Tory chair of the Commons justice committee, Sir Bob Neill.

The Neill amendment, which was voted on instead of the genocide amendment, hands the power to decide whether a country is carrying out genocide to parliamentary committees instead of judges.

It was approved by MPs who voted 318 in favour to 303 against, with Johnson’s working majority cut from 87 to just 15, signifying a major proxy Conservative rebellion of 31 backbenchers.

Former Tory leader and prominent rebel Sir Iain Duncan Smith said: “The government has run out of arguments and is now using arcane procedural games which demean our democracy and the House of Commons.”

Later, in the Commons debate on the issue, he added: “This little dispute’s a little bit like Handforth Parish Council and it’s always a good idea to read the standing orders. 

“I read them and it told me what happened. The government deliberately has blocked this.”

Duncan Smith added: “I say to my honourable friends, I’ve been here long enough, and I simply say I think this is beneath them [the government] and I wish they had thought again and they don’t try this one again.”

He rejected the idea of giving select committees the power to rule on genocide rather than impartial judges.

The former cabinet minister told MPs: “When we need an impartial taking of evidence and a judgment, we turn not to select committees on this, let’s take for example Saville, Grenfell, Hillsborough, or any of the other cases, we turn to a judge.

“Why do we do that? One, because we assume they’re impartial. Two, because they are trained to take evidence and to deal with evidence – we are not here, we are partial, that’s why we’re here, we are select committees and we have prejudices.”

Fellow rebel Imran Ahmed Khan said: “I am disappointed by the cynical manipulation of procedure which seeks to deny the House the right to vote on an issue it clearly wishes to divide on.”

For Labour, shadow trade secretary Emily Thornberry suggested that future generations will wonder why “procedural parliamentary games” are being played on an issue “as serious and momentous as the genocidal crimes being committed against the Uighurs in China”.

But trade minister Greg Hands claimed countries committing genocide could enjoy a propaganda boost if a UK court could not prove the allegations.

He insisted it should be for parliament, initially through committees, to “take a position on credible reports of genocide”.

Hands told the Commons: “Genocide is notoriously hard to prove with a high legal threshold.

“If a judge was unable to make a preliminary determination on genocide, which is highly probable, it would be a huge propaganda win for the country in question – effectively allowing that state to claim it had been cleared by the UK courts.”

A Labour source said the House of Lords was likely to send the bill, which sets out a framework for post-Brexit free trade deals, back to the Commons with the genocide amendment reinserted.

It sets up another big Tory split on the issue in the weeks to come.