Nine seamen were rescued after a cargo ship sunk during storms in southern Thailand, which also left 31 Navy sailors missing at sea in a separate incident.

The crew of the Santhat Samut 2 had set sail from Surat Thani province for Chonburi when they encountered waves reaching up to four metres high on December 17.

Local media reported the churning seas 'broke the container chains', causing the ship to lose control near the Phum Riang Bay in Surat Thani.

The nine people onboard fired a flare to call for help before jumping onto lifeboats and escaping the sinking ship carrying 36 containers of rubberwood.

They rowed towards the shore where they were helped by local fishermen.

Surat Thani officials had issued stay-in-port orders for vessels moving through the Gulf of Thailand due to the bad weather, but the crew had already left by the time the advisory was announced on December 18.

No casualties were reported. Authorities said they will be conducting further investigations into the accident.

Thailand's Meteorological Department warned of 'four metre high waves' battering regions along the eastern-facing coastline.

Officials said the storms and heavy rain would continue until December 20 in Surat Thani, Nakhon Si Thammarat, Phatthalung, Songkhla, Pattani, Yala and Narathiwat along the border with Malaysia.

Storms at sea over the weekend have caused chaos for several vessels. The navy warship HTMS Sukhothai sank in the Gulf of Thailand off the coast of Prachuap Khiri Khan province leaving 31 people missing at sea on Sunday while an oil tanker was beached in Songkhla province.