"The search will continue tonight with two naval ships," Radjasa told MetroTV after arriving in Semarang, where relatives searched lists of survivors.
He said "we are using our maximum efforts to rescue as many people as possible".
He later told ElShinta radio that the ship was built in 1990 and serviced earlier this year, "so it should not have had any problems".
"The huge waves had caused the ship to sink," he said.
The Senopati Nusantara (Archipelago Commander) had been due in Semarang late on Friday after what should have been a 19-hour voyage.
Navy ships and helicopters earlier found some of the survivors stranded on the nearby island of Bawean, but could not find any trace of the ship, ElShinta radio said.
An airforce C-235 patrol aircraft was also searching for survivors.
The ferry left Kumai in Central Kalimantan province on Borneo island en route to Semarang in Central Java 420km away, and sank near Mandalika island off the Java coast. It was not known exactly where it went down.