Immigration chief says the group was sent back on three Myanmar navy ships and do not include Rohingya or asylum seekers.
Malaysia has deported 1,086 Myanmar nationals, despite a court order temporarily halting the repatriation amid concerns the group could be at risk if they are returned to military-ruled Myanmar.
The statement did not mention the court order or explain why only 1,086 were deported instead of 1,200.
“The government must respect the court order and ensure not one of the 1,200 individuals is deported today,” she said in a statement following the court ruling.
“This plan puts lives at risk and gives undeserving legitimacy to the abusive military coup in Myanmar.”