Malaysia faced calls Monday to halt the deportation of 1,200 Myanmar nationals on navy ships to their homeland weeks after a coup, with the United States the latest to voice concerns.

The migrants, who include members of vulnerable minorities, are set to be repatriated Tuesday aboard three vessels sent from Myanmar, where the military seized power at the start of February.

The ships arrived at the weekend and docked at a naval base at Lumut, on Malaysia's west coast.

The US embassy in Kuala Lumpur told AFP it had expressed concerns and urged authorities to allow the UN refugee agency access to the detained Myanmar nationals, which would allow them to assess if any were asylum seekers.

The refugee agency has said at least six among those to be deported are registered with the body and in need of international protection, but it has not had access to the vast majority of them. 

Amy Smith, executive director of Fortify Rights, said that the planned deportation "puts lives at risk and gives undeserving legitimacy to the abusive military coup in Myanmar".

"This is a time to extend protection to people fleeing Myanmar and grant the UN access, not put them into the hands of a military junta with a long track record of serious human rights violations."

Among those to be deported are members of the Christian Chin minority and people from conflict-riven Kachin and Shan states, according to Lilianne Fan, international director of the Geutanyoe Foundation which works with refugees.

Officials say those being repatriated have committed offences including overstaying their visas and no members of the Rohingya Muslim minority, who are not recognised as citizens in Myanmar, will be repatriated. 

Malaysia is home to millions of migrants from poorer parts of Asia who work in low-pay jobs such as construction. As well as Myanmar, they come from countries including Bangladesh and Indonesia.