The boat was carrying 105 people - 93 Chinese tourists and 12 crew and guides - when it hit trouble on the Andaman Sea - sparking a rescue attempt in the dark.
Another boat also overturned off Phuket on Thursday.
Officials said that divers reported seeing at least another ten bodies inside the sunken hull of the Phoenix tourist vessel, which sank yesterday afternoon. Both were pulled safely from the sea, according to the police report.
A Chinese consular official arrived at the operations center in Phuket to monitor the rescue effort.
The governor of southern Phuket, Noraphat Plodthong, said: 'There are 53 people missing.
Thai rescue personnel carry a body bag bearing the recovered body of a passenger from a capsized tourist boat at Chalong pier in Phuket on July 6, 2018.
The dead were found drifting face down in the water, still wearing life jackets, several kilometres from where the Phoenix sank after being hit by five-metre high waves in a storm on Thursday evening.
Search and rescue operations, suspended overnight, resumed on Friday morning.
They said they were providing food, shelter and water to the people, and if the weather did not clear, larger boats belonging to the navy would be sent to retrieve them.
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There are some Chinese tourists on board, the consulate-general said, and they are mostly one-day individual visitors or staff and their families of a Chinese company.
The boat was one of three to encounter difficulties at sea in the area on Thursday, the navy said.
"The Tourist Police warned businesses in Phuket already to not take boats out from shore, but they violated this order by taking foreign tourists out", he said.
"What is imperative is to search for the missing", a statement from the embassy said Friday.
Some of the bodies were found by divers who entered the wreck on Friday and others were floating in the water, navy official Narong Aurabhakdi said.
Phuket officials had earlier issued a warning of severe weather until next Tuesday, including heavy rain and winds.
Thailand is in the midst of its monsoon season, which begins in May and usually ends in October and often generates high winds and flash storms in coastal areas.
Thai television broadcast images of dozens of divers, some carrying scuba gear, searching for missing passengers and crew at the scene, while more rescuers waited on standby at a pier nearby.