David Cameron indicated on Thursday evening that Britain would not take part in military action against Syria after the British government lost a crucial vote on an already watered-down amendment that was designed to pave the way to intervention in the war-torn country.

In a devastating blow to his authority, the prime minister lost a government motion by 272 votes to 285 – an opposition majority of 13 – after scores of Tory MPs voted with Labour.

Ministers had thought they were secure after a Labour amendment was defeated, in the first vote of the night, 332 votes to 220, a government majority of 112.

Labour claimed that the government ran into trouble when deputy prime minister Nick Clegg struggled, in the closing minutes of the debate, to answer concerns on all sides of the house that the government motion would have taken Britain closer to joining a US military operation against the Assad regime in Syria after last week's chemical weapons attack.

One MP shouted "resign" as the results were read out by the speaker. David Cameron said the government would respect the decision of parliament which means that Britain will not take part in military strikes against Syria.

Asked by Labour leader Ed Miliband for an assurance that he would not use the royal prerogative to sanction British involvement in the military action, the prime minister told MPs: "I can give that assurance. Let me say, the House has not voted for either motion tonight. I strongly believe in the need for a tough response to the use of chemical weapons, but I also believe in respecting the will of this House of Commons.

"It is very clear tonight that, while the House has not passed a motion, it is clear to me that the British parliament, reflecting the views of the British people, does not want to see British military action.

"I get that and the government will act accordingly."

The vote came after Cameron and Ed Miliband were embroiled in one of the most serious disagreements on foreign policy in a generation when Craig Oliver, Cameron's director of communications, accused Miliband of giving succour to the Syrian regime by refusing to agree to a Commons vote on military action. Labour said the language used was "infantile".

Philip Hammond, the defence secretary, then used the same word to warn of the dangers of a disunited parliament. Hammond told Channel 4 News: "I'm disappointed with Ed Miliband's behaviour frankly. Anything that stops this from giving a clear united view of the British parliament tonight will give some succour to the regime."

The intervention by Hammond came amid fury in Downing Street after Miliband had forced the prime minister on Wednesday to offer MPs a second vote to authorise British involvement in a military strike. This would have to be delayed until after the UN weapons inspectors have completed their report.

The shock result means that Cameron becomes the first British prime minister in decades unable to deliver British troops to a joint military operation with the US. Whitehall sources had said Barack Obama was willing to show some patience for Britain but he would need to launch strikes against Syria before he leaves for the G20 summit in Russia next Tuesday. The New York Times reported on Thursday night that Obama is preparing to act alone at the weekend.

Earlier, the prime minister had tried to make a virtue out of conceding that MPs were to be given a second vote on any military action by saying that he had allowed UN time and giving parliament a major say on the crisis.

Cameron moved to build the case for action by releasing a three-page assessment of the Joint Intelligence Committee which said it was "highly likely" the Assad regime launched the chemical weapons attack. But the document failed to ascribe a motive to the regime for the attack.

Downing Street also released a government summary of the legal advice by the attorney general, Dominic Grieve, which said military action would be lawful "under the doctrine of humanitarian intervention".

Opening the debate in a packed Commons, the prime minister said the attorney general had delivered a clear judgment. But he acknowledged that the intelligence agencies had not delivered a definitive verdict.

Philippe Sands, a leading expert in international law, said the document failed to provide a "sound or persuasive legal argument" in favour of military action.

Cameron pointed out that the JIC assessment concluded that the Assad regime had used the weapons on 14 occasions, warning of the dangers of failing to take action to deter future attacks. He told MPs: "I think we can be as certain as possible that a regime that has used chemical weapons on 14 occasions and is most likely responsible for this large-scale attack will conclude, if nothing is done, that it can use these weapons again and again on a larger scale and with impunity.

"People talk about escalation; to me, the biggest danger of escalation is if the world community – not just Britain, but America and others – stands back and does nothing. I think Assad will draw very clear conclusions from that."

Cameron's voice cracked with emotion as he spoke of the videos of victims after the attack. He said: "There are pictures of bodies with symptoms consistent with that of nerve agent exposure, including muscle spasms and foaming at the nose and mouth. I believe that anyone in this chamber who has not seen these videos should force themselves to watch them.

"One can never forget the sight of children's bodies stored in ice, and young men and women gasping for air and suffering the most agonising deaths – all inflicted by weapons that have been outlawed for nearly a century."

Miliband said the prime minister had failed to prove definitively that the Assad regime was responsible for the attack as he intensified the pressure on Cameron by pressing an alternative Labour amendment to a vote.

The Labour leader told MPs: "There will be some in this house who say that Britain should not contemplate action even when it is limited, because we do not know precisely the consequences that will follow.

"As I said, I am not with those who rule out action, and the horrific events unfolding in Syria ask us to consider all available options, but we owe it to the Syrian people, to our own country and to the future security of our world to scrutinise any plans on the basis of the consequences they will have."

The differences between Cameron and Miliband – and the bitter exchanges between their surrogates on the airwaves – showed that the general convention of a bipartisan approach between the frontbenches on overseas military operations is being stretched by Syria. The opposition parties supported the government, with qualifications, during the two most contentious wars of the last 30 years – the Falklands in 1982 and Iraq in 2003.

The row also raises the prospect of a redefinition of the Anglo-American "special relationship". Prime ministers from Margaret Thatcher have made a point of ensuring that they can deliver British troops, when requested, to preserve the wide ranging intelligence co-operation.

But military commanders have also been contemplating the damage that might be done to the relationship if Britain is left on the sidelines.

The Ministry of Defence refused to discuss the developments.

Sources in Whitehall, however, confirmed that the Americans had wanted to orchestrate a series of missile strikes "as soon as possible". Sending six RAF Typhoon fast jets to Cyprus on Thursday morning was the last piece of a complex jigsaw before the operation.

They said America had "no real need to wait for Britain", and indicated the US would be able to undertake a limited campaign without the UK's proposed contribution – thought to consist of a small number of Tomahawk cruise missiles being launched from one of the Royal Navy's Trafalgar class submarines.

"We have had no indication yet that the Americans have decided to change their plans and wait for the UK," said one insider. "There is certainly nothing to stop the US doing this without us. The US could go without British support but that could be hugely damaging to Britain's reputation as a global power."

Another Whitehall source added: "Could the US do it without us? Yes they could. Would they want to do it without the UK? No, they wouldn't. They would prefer any action against Syria to be a collaborative effort between allies."

However, British officials believe the window for action against Syria may be closing fast; President Obama is due to meet President Putin at the G20 summit in St Petersberg next Tuesday, and Washington wants to have concluded operations by then.

The decision to send the Typhoons to Cyprus is regarded as a prudent defensive measure, whether the UK is involved in any forthcoming attack.

The island is within range of President Assad's air force — and potentially his Scud missile batteries. Though an attack on Cyprus is thought unlikely, the island hosts some of the UK's most important surveillance and listening stations, which provides valuable intelligence to the UK and the US about events across the Middle East.

An RAF spokesman said: "Six RAF Typhoon interceptor fast jets are deploying to Cyprus. This is purely a precautionary measure to ensure the protection of UK interests and the defence of our Sovereign Base Areas at a time of heightened tension in the wider region.

"This is a movement of defensive assets operating in an air to air role only. They are not deploying to take part in any military action against Syria."