Malaysia on February 23 deported more than 1,000 Myanmar detainees back to their strife-torn homeland just weeks after a coup, despite a court order halting the repatriation and a storm of criticism.

The migrants, whom activists say include vulnerable asylum seekers, departed on three Myanmar navy ships from a Malaysian military base after arriving on packed trucks and buses under police escort.

The US, UN and rights groups had criticised the plan, while hours before the deportation a Kuala Lumpur court ordered it be temporarily halted to allow a legal challenge.

Activists were set to argue it should not go ahead as Malaysia would breach its international duties by deporting vulnerable people, and the Myanmar military’s seizure of power put them at even greater risk.

But the vessels later set sail carrying 1,086 detainees, with authorities giving no explanation as to why the court order had been ignored.

Amnesty International, one of the groups that had brought the legal challenge, said pushing ahead with the repatriation in defiance of the ruling was “inhumane and devastating”.

“This life-threatening decision has affected the lives of more than 1,000 people and their families, and leaves an indelible stain on Malaysia’s human rights record,” said Katrina Jorene Maliamauv, executive director of the group’s Malaysian office.

Phil Robertson, deputy Asia director for Human Rights Watch, said Malaysia had “sent them back into the hands of a military junta known for persecuting those who flee the country for political reasons”.

Malaysian immigration chief Khairul Dzaimee Daud had offered assurances no members of the persecuted Rohingya minority – not recognised as citizens in Myanmar – or asylum seekers had been repatriated.

“All of those who have been deported agreed to return of their own free will, without being forced,” he said.

Rights groups have however raised doubts over authorities’ claims no asylum seekers were among those sent back, as the UN has not been able to do a proper assessment.

Officials insist those sent back had committed offences such as overstaying their visas, and the deportation was part of their regular programme of repatriating migrants from poorer parts of Asia.

Malaysia is home to millions of migrants who work in low-paying jobs such as construction. About 37,000 foreigners were repatriated last year.