Three men, believed to be crew members of the vessels that caught fire at Tanoto Shipyard on Tuesday night, are missing.
The Straits Times understands search and rescue operations to find them are underway.
One man was rescued on Tuesday night, after four vessels caught fire at the shipyard off Shipyard Road in Jurong.
The Singapore Civil Defence Force (SCDF) was alerted to the incident at 9.19 pm on Tuesday.
Officers arrived to find four vessels on fire, all berthed alongside each other. Some were believed to be tugboats.
One of the vessels was fully engulfed in flames and eventually sank.
The man was rescued from the blaze with burn injuries and taken to the Singapore General Hospital.
It took the officers 90 minutes to get the blaze under control, an SCDF spokesman told The Straits Times. Four fire engines, two Red Rhinos, six supporting vehicles, two ambulances and two marine fire vessels were deployed.
The SCDF used eight hand-held water jets from the fire engines and two foam monitors from one of the marine fire vessels.
Investigations are underway.