Navy official Narong Aurabhakdi said some of the bodies were found by divers who entered the wreck Friday and others were floating in the water.
After the boats overturned on Thursday due to adverse weather conditions, 48 passengers and Thai crew members were rescued.
As the seas calmed on Friday, divers were transporting the bodies of the dead, including at least one child, from smaller boats to a larger ship taking part in the search effort.
Rescue efforts are underway for dozens of passengers who went missing Thursday after two boats capsized off Thailand's resort island of Phuket in what appear to be separate incidents, according to a police spokesman.
Thailand's navy said early Friday afternoon that nine bodies of Chinese tourists were being brought to Phuket. "We ask the Thai side to mobilize all possible forces and waste no time in searching for the Chinese citizens that are still missing".
"It's very hard to see.it's traumatic, it's tragic but the best thing to do, our job as divers, is to bring back the bodies to their families", diver Philip Entremont told reporters on Saturday.
The boat was carrying 105 people, including 93 tourists, 11 crew and one tour guide when it toppled in 5-meter (16-foot) -high waves on Thursday evening.
Lt Gen Sorasak Yenpraem of Region 8 Police said that officers had already take statements from 40 witnesses.
Thai authorities say the death toll in a boat accident off the coast of Phuket has climbed to 17.More news: Trump picks conservative Kavanaugh as US Supreme Court nominee
Prime Minister Prayuth Chan-ocha, the leader of Thailand's military government, expressed his "sympathies and deepest condolences" to the families of the dead.
On Saturday, local police accused the captain of one ship of negligence causing death, although he reportedly denied the claim.
Rear Admiral Charoenpol Kumrasri, a deputy commander of the Thai navy, who is helping to lead the rescue effort, said he was confident divers would complete their search of the sunken vessel by Saturday.
"The 12 bodies are on the way to Vachira Phuket Hospital for identification", a statement from the Public Health Ministry in Bangkok said.
The death toll from a boat accident near the Thai holiday island of Phuket has risen to 21.
Thai officials were rushing to cope with some of the logistics of the aftermath of the sinking.
The government of the eastern Chinese city of Haining in Zhejiang province said on its official microblog account that it received a distress alert sent by phone text message from the head of the Haining Haipai Furniture Co.
Mr Gao Kai, who arrived in Phuket on Saturday, said the bodies of his eight-year-old daughter and seven-year-old nephew were identified on Saturday, but he was still waiting for news of his wife, sister and brother-in-law. The group had booked their tours to the islands online on their own, said the posting.
He said department officials have been instructed to provide full cooperation for the search and rescue operation.