The two survivors, a husband and wife, said the incident occurred on Tuesday night, but locals only reported it to the Malaysian maritime agency a day later.
The Malaysian Maritime Enforcement Agency said in a statement late on Wednesday that it had launched a search and rescue operation, but that the 24 hour delay in being notified would make the search difficult.
"It is feared that 13 victims including the skipper and a baby has drowned. Search and rescue efforts will be continued to find any survivors," said maritime territory director Mohd Zubil Mat Som.