Rescuers carry an injured person on a stretcher after a boat capsized off the tourist island of Phuket, Thailand July 5, 2018 in this still image taken from video.
Phuket Marine Office Chief Surat Sirisaiyat said his office has been informed by the Meteorological Department that heavy rains and strong winds will hit the southern part of Thailand on the Andaman Sea with waves of up to three metres predicted for Friday.
Around 48 passengers from the first boat - which was carrying mostly Chinese tourists - have been rescued, but another 49 are now missing.
The two people still missing were named as boat mechanic Aroon Habinsun and 30-year-old Chinese tourist Sun Hua Fang.
But officials said the 39 Chinese and European tourists forced to abandon that boat were rescued and have returned to land.
The body of one of the passengers, believed to be a Chinese holidaymaker, was pulled from the sea late Thursday and brought to shore, shortly before the search was called off for the night. "We have sent boats to help", Rear Admiral Somnuk Prempramote, commander of the Royal Thai Navy Region 3.
A late report from the Thai PBS television station said the body of a man wearing a life jacket from the larger vessel had been recovered.
One of the vessels - reportedly returning to Phuket from Koh Racha - was carrying 90 passengers when it overturned.
Thailand is already making worldwide headlines after 12 boys and their junior football coach were found alive this week after becoming trapped inside a cave in the country's north.
Severe weather is forecast in the area until next Tuesday.
But as details dripped through overnight, governor Noraphat said two passengers were still unaccounted for from another stricken ship.
They are said to have been a group of Chinese tourists.
Thailand is in the middle of its monsoon season which brings with it adverse weather conditions.