Seven pirates armed with guns and other weapons assaulted sailors of the South Korean-registered CK Bluebell, about 160km from the entrance of the Singapore strait at 4.25 am.
No casualties were reported from the attack, they said, but some sailors sustained minor injuries, such as bruises, during their confrontations with the pirates.
The pirates made off with US$13,000 in cash
The CK Bluebell, en route to Incheon after departing from Brazil, resumed its normal navigation after the attack, they said.
"Ordinary freighters navigate at a speed below 15 knots. But a speed boat operated by the pirates approached the freighter at a speed above 20 knots.
"Afterwards, seven weapon-wielding pirates got on board and assaulted the sailors for about 30 minutes," a ministry official said.
The official said the ministry had delivered news of the pirate attack to all Korean-registered vessels near the Singapore Strait and asked them to be alert.