The Tanoto Shipyard fire started from a tug boat and later spread to three others that were adjacent to it, said the Ministry of Manpower (MOM) on Wednesday.
"Officers from MOM's Occupational Safety and Health Inspectorate have commenced investigations into the incident," said the ministry.
"Preliminary findings show that a fire had started on a tug boat and spread to three adjacent tug boats.
"Four foreign crew members were injured and conveyed to hospital."
Meanwhile, the Maritime and Port Authority of Singapore (MPA) is co-ordinating a seaward search and rescue operation for the three persons who are unaccounted for.
Two MPA and a Police Coast Guard craft are involved in the operation.
"While investigations are ongoing to ascertain whether there was any work in progress before the fire broke out, MOM has instructed the occupier to stop all work at the shipyard," said the MOM.
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 SCDF said in its latest update that the fire was extinguished at 4.30am on Wednesday.