Amnesty International, one of the groups that had brought the legal challenge, says pushing ahead with the repatriation in defiance of the ruling is "inhumane and devastating."
Malaysia has 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 United States, the United Nations 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.
Defying court decision
The Malaysian court ordered a halt to the planned deportation of 1,200 Myanmar migrants to hear an appeal by human rights groups, which say refugees, asylum seekers, and minors were among those being sent back.
On Tuesday, the court order, following a legal bid by Amnesty International Malaysia and Asylum Access Malaysia, came just after the migrants were transported to a naval base where three Myanmar military ships were waiting to take them home.
Amnesty urged the government to give the UN High Commissioner for Refugees access to the 1,200 migrants and all immigration detention centers in general, which Malaysia's government has denied since August 2019.
Malaysian immigration office earlier said there were no UNHCR cardholders or ethnic Muslim Rohingya refugees in the group, who were held for offenses including not having valid travel documents, overstaying their visas and violating social visit passes.
But the two rights groups in their legal filing named three people registered with the UNHCR and 17 minors who have at least one parent still in Malaysia.
The UNHCR has separately said there were at least six people registered with it among the group due to be deported.
Amnesty and Asylum Access have said the repatriation is tantamount to legitimizing ongoing human rights violations by Myanmar’s military and would put the migrants at risk of further persecution, violence and even death.
No members of Rohingya repatriated
"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 Amnesty International 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.
Authorities earlier said 1,200 detainees were to be deported, and it was not clear why the final number was lower.
Asylum Access Malaysia & Amnesty International Malaysia are seeking a court intervention to halt the deportation of 1,200 people to Myanmar.— BFM News (@NewsBFM) February 22, 2021
This follows information that asylum seekers, refugees & children with at least 1 parent still in Malaysia are among those being deported. pic.twitter.com/BOaYnjQAXK
Migrants and refugees in Malaysia
A group of 27 Malaysian lawmakers and senators also sent a letter to Prime Minister Muhyiddin Yassin on Sunday urging him to halt the deportation.
There was no response from the premier's office.
Malaysia doesn’t recognise asylum seekers or refugees, but has allowed a large population to stay on humanitarian grounds. It is home to some 180,000 UN refugees and asylum seekers, including more than 100,000 Rohingya and other Myanmar ethnic groups.
More than 700,000 Rohingya have fled from Myanmar since August 2017, when the military cracked down in response to attacks by a rebel group. The security forces have been accused of mass rapes, killings, and the burning of thousands of homes.
Malaysia initially expressed "serious concern" at the February coup, but just days later news emerged it had accepted an offer from the Myanmar junta to send warships to repatriate the detainees.