Malaysia has returned nearly 1,200 migrants from Myanmar in defiance of a court order and appeals from human rights groups to halt the process.

The Myanmar nationals were bused in from around the country and loaded onto three navy ships sent to retrieve them by Myanmar's ruling junta, which seized power in a coup earlier this month.

The action followed a stay issued by the Kuala Lumpur High Court putting the deportation stay of the 1,086 refugees on hold pending a Wednesday hearing.

Malaysia maintains that the deportees were detained for immigration offenses.

The director-general of the country's immigration department says no Rohingya people or asylum-seekers were part of the group sent back to Myanmar.

"All of those returned had agreed to be sent back voluntarily without being forced by any party," Khairul Dzaimee Daud said in a statement, without explaining the government's reasoning for defying the court order.

Amnesty International and another rights group, Asylum Access, say the migrants returned include some from ethnic groups that have suffered persecution in Myanmar in the past. They also said that about a dozen children with at least one parent in Malaysia are among the deportees.

Amnesty and Asylum Access were "shocked at the authorities' disregard for a court order to stop the deportation," Lim Wei Jiet, a lawyer for the two rights groups, told The Australian.

"The haste in which this entire operation is executed, despite the judiciary's clear order to do otherwise, raises more questions on the motives of the parties involved," Lim said, adding that the deportations risked legitimizing Myanmar's junta and exposing the country's ethnic minorities to further persecution at the hands of the military.

After the court's decision, but before news of the deportations became known, Amnesty's Malaysia director, Katrina Maliamauv, called on Malaysia "to reconsider its plans to send this group of vulnerable people back to Myanmar, where human rights violations are currently dangerously high."

She has accused the country of detaining refugees in "horrific conditions."

"But the options for people and their families cannot be between indefinite detention or putting their lives at risk by returning to a possibly dangerous situation," Maliamauv said in a previous statement.

Despite not be a signatory to the 1951 Refugee Convention, predominately Muslim Malaysia has vowed not to deport Rohingya people or refugees registered with the U.N. High Commissioner for Refugees. It has allowed some 180,000 United Nations refugees and asylum seekers, including about 100,000 Rohingya and members of other Myanmar ethnic groups, to remain on humanitarian grounds, according to The Associated Press.

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