A Labour demand for the UK government to withdraw support for the Saudi-led coalition in the 18-month Yemen civil war failed on Wednesday when a substantial number of Labour backbenchers either stayed away or abstained.

In a Commons debate, the shadow foreign secretary, Emily Thornberry, said the government should withdraw support from the Saudi coalition until an independent UN investigation had examined whether the Saudi bombing campaign, which has seen the deaths of thousands of Yemeni civilians, was in breach of international humanitarian law.

The Labour front bench, partly due to resistance from unions with membership in the defence industry, did not explicitly call for a suspension of UK arms sales to Saudi Arabia until the independent inquiry reported. The Labour call for ministers to withdraw support from the Saudi coalition was defeated by 283 to 193, suggesting that scores of Labour MPs did not vote.

The foreign secretary, Boris Johnson, rejected any suspension of arms sales, saying other western countries would “happily supply arms” to Saudi Arabia without the same protections should Britain suspend its sales. He added that suspending arms sales would “at a stroke” eliminate Britain’s diplomatic influence on the Yemen conflict, in which the Saudi Arabian-led coalition has been accused of war crimes. He also said it was right that Saudi Arabia first conducted its own investigation.

In a compromise on 30 September, the UN Human Rights Council in Geneva, with the backing of the UK, did not support an immediate independent UN inquiry, but instead called for UN experts to be given a role in assisting an existing Yemen-led inquiry.

Johnson’s foreign office deputy, Tobias Ellwood, accepted that Saudi Arabia’s own internal inquiries into its bombing campaign had been unduly slow. He added that he expected a specific senior Saudi officer to be subject to a court-martial for failing to follow internal procedures when Saudi planes on 8 October bombed a funeral in Yemen’s capital, killing more than 140 people and wounding hundreds of others.

Johnson warned the Saudis they “should be in no doubt that we in this country are monitoring the situation minutely and meticulously, and will continue to apply our established criteria for granting licences with fairness and rigour, and in full accordance with UK law”.

But he added that if the UK suspended arms sales, “be in no doubt that we would be vacating a space that would rapidly be filled by other western countries who would happily supply arms with nothing like the same compunctions or criteria or respect for humanitarian law. And more importantly, we would at a stroke eliminate this country’s positive ability to exercise our moderating, diplomatic and political influence on a crisis where there are massive UK interests at stake.”

Johnson also claimed Thornberry had “substantially retreated” from the opposition’s motion, specifically over whether to suspend weapons sales.

He said: “Under questioning … as to whether or not she would support the immediate suspension of arms sales to Saudi Arabia and the Saudi Arabian-led coalition forces, as is specified in this motion in her name, she refused to say that she would”.

But Thornberry disagreed, saying the Labour motion simply called on ministers to suspend support to the coalition until it has been determined whether they had been responsible for violations of international humanitarian law.

John Woodcock, the Labour MP for Barrow, asked Thornberry how UK withdrawal of support for the coalition – focused on training Saudis in compliance with international humanitarian law – would create fewer civilian casualties.

Thornberry answered that the overwhelming evidence suggested that Saudi Arabia was not listening to UK advice, and that the Saudis had only produced nine reports on its bombing incidents, and could not provide a timetable for the completion of further reports. She said it was a clearly disturbing trend that two coalition forces were in reality operating in Yemen.

Thornberry said one command centre based in the capital Riyadh ran pre-planned operations based on strong intelligence under the direction of the Americans and UK advisers. The other centre, operating out of southern Saudi Arabia, “carried out dynamic, reactive operations often on the basis of sketchy evidence, often without thinking through the so-called ‘collateral damage’, and inevitably often with significant civilian casualties.

“Of course, if it is the case that any coalition forces are acting in a reckless or indiscriminate manner when it comes to air strikes in civilian areas, it would itself be a clear violation of international humanitarian law and cause this whole house grave concern.”

Thornberry said Ellwood had described the funeral bombing as a “deliberate error”, raising the prospect of “intentional targeting of civilians by elements of the coalition forces”. She added: “When we say one thing about Russia and Aleppo but we say another thing about Riyadh and Yemen, what the rest of the world hears is hypocrisy and double standards.

“While Saudi Arabia will remain a valued strategic security economic ally, our support for their forces in Yemen must be suspended until alleged violations of international humanitarian law in that conflict have been fully and independently investigated, and until the children of Yemen have received the humanitarian aid they so desperately need.”

Chris White, the Conservative chairman of the all-party select committee on arms export controls, also said there had been violations of international humanitarian law in Yemen justifying an independent, UN-led investigation, and the suspension of arms sales pending the inquiry.

He questioned whether civilian casualties at such a level could be regarded as a mistake. He said whether the mistakes were intentional or not, they represented a breach of humanitarian law, and the default position of the government should be to pause sales until it was satisfied with the conduct of the campaign.