Malaysia's government faced mounting criticism from opposition MPs and rights groups Wednesday over its decision to deport over 1,000 Myanmar nationals in defiance of a court order. 

The migrants, whom activists say include vulnerable asylum seekers, departed Tuesday on Myanmar navy ships from a Malaysian military base back to their homeland, just weeks after a coup.

Rights groups had fiercely criticised the plan, and hours before the deportation the Kuala Lumpur High Court ordered it be temporarily halted to allow a legal challenge from activists. 

But officials pushed ahead regardless, repatriating 1,086 migrants and offering no explanation as to why the court's instructions were ignored. 

In a joint statement, four opposition lawmakers condemned the "inhumane" deportation and suggested government officials could be held in contempt for ignoring the legal ruling. 

"This act... is a clear display that the Malaysian government does not respect the ongoing court process and has put Malaysia in a bad light on the human rights front," they said. 

Amnesty International, one of the groups that challenged the deportation, said the government "owes an explanation to the people of Malaysia as to why they chose to defy the court order".

"These dangerous deportations have not been properly scrutinised and put individuals at grave risk," said Katrina Jorene Maliamauv, executive director of Amnesty's Malaysia office.

More than 100 migrants originally to be deported are believed to have been left behind, with officials offering no explanation as to why. On Wednesday the High Court ruled those remaining should be not sent back as NGOs challenge the repatriation.

Malaysian immigration officials insisted there were no members of the persecuted Rohingya minority -- not recognised as citizens in Myanmar -- or asylum seekers among those repatriated. 

But rights groups have raised doubts over authorities' claims there were no asylum seekers among the deportees.

Authorities have since 2019 blocked the UN refugee agency from immigration detention centres, meaning they cannot assess which migrants have genuine asylum claims and should be allowed to remain in Malaysia.

It is rare for NGOs to challenge repatriations but in the latest case, they were particularly concerned about the worsening human rights situation in Myanmar since the coup.