RAF Reaper drones were involved in the weekend airstrike that killed at least 62 Syrian government troops and threatened the fragile truce in the country, the Ministry of Defence has said.

An unspecified number of weapons were fired from the drones capable of firing 500lb laser guided bombs and Hellfire missiles, it added.

The British military said it was cooperating fully with an investigation by the US-led coalition into the incident, which led to dozens of soldiers being killed and injured, according to Syrian government reports.

Australian, Danish and US air forces were also involved in the raid.

An MoD spokesman said: “We can confirm that the UK participated in the recent coalition airstrike in Syria, south of Deir ez-Zour on Saturday, and we are fully cooperating with the coalition investigation.

“The UK would not intentionally target Syrian military units. It would not be appropriate to comment further at this stage.”

The incident is likely to be the most serious mistake by UK air forces since the House of Commons sanctioned the extension of attacks from Iraq to Syria last December.

Until the end of August the Reaper drones had flown 547 sorties in Syria, releasing weapons in 29 of these, including 45 Hellfire missiles. The raids are supposed to be confined to attacks on Islamic State (Isis) fighters.

The raid prompted a furious response from Russia and Syria, and led to allegations that the airstrikes on the Syrian soldiers could not have been mistaken.

Syria’s president, Bashar al-Assad, described the attack as “flagrant aggression”.

Russia’s UN ambassador, Vitaly Churkin, said the bombing did not look like an honest mistake. Photograph: AL Jones/Pacific/Barcroft Images

The Russians called an emergency meeting of the UN security council to discuss the incident, a move describe by the US ambassador to the UN, Samantha Power, as a stunt.

Russia’s UN ambassador, Vitaly Churkin, said: “It is highly suspicious that the US chose to conduct this particular airstrike at this time,” adding that it did not look like an honest mistake.

The US military has not confirmed the strikes against the Syrian troops but has suggested it was carrying out a raid against Isis fighters in eastern Syria.

Syria’s weeklong ceasefire, brokered by the US and Russia, was in any case in growing doubt amid claims of repeated violations by both sides and the UN’s failure to deliver aid to eastern Aleppo.

The Australian prime minister, Malcolm Turnbull, confirmed that his country’s aircraft had been involved, but pulled out when Russian officials advised the targets may have been Syrian military personnel.

“We regret the loss of life and injury to any Syrian personnel affected,” Turnbull told reporters in New York, where he will attend the annual United Nations genera assembly.

He said Australia’s rules of engagement were to target Isis, but that the environment in Syria was very complex.

“You’ll find over the next little while no doubt arguments or issues about why there wasn’t more coordination or who was meant to be advising who,” he said.

Turnbull said it remains to be seen whether the incident would jeopardise the Syrian ceasefire.

The location of the strike was in an area the coalition has struck in the past, US Centcom officials said. Coalition members in the air operations centre had earlier informed Russian counterparts of the upcoming strike.

“It is not uncommon for the coalition air operations centre to confer with Russian officials as a professional courtesy and to deconflict coalition and Russian aircraft, although such contact is not required by the current US-Russia memorandum of understanding on safety of flight,” officials said in a statement.

“Syria is a complex situation with various military forces and militias in close proximity, but coalition forces would not intentionally strike a known Syrian military unit,” the officials said. “The coalition will review this strike and the circumstances surrounding it to see if any lessons can be learned.”