The boat was heading to Indonesia's Batam island when it sank in rough seas about three hours after it left shore, Amran said.
Those missing include women and children, as search and rescue operations continued.
"The condition of the boat was believed to be questionable," Amran said.
Three of the survivors were rescued by passing fishermen, while another was saved by authorities alerted by the fisherman.
"Only four of those on board were rescued by fishermen and MMEA after floating 15 hours in the sea," Amran said, adding the four men have been hospitalised.
Boating accidents off Malaysia's coast are common as thousands of people from poorer regional neighbours come to work illegally in the relatively affluent country.
Many Indonesians try to leave the country furtively during Ramadan to return home to celebrate Eid al-Fitr, the end of the Islamic fasting month.
Authorities said last month they were beefing up patrols.