A ferry on the route between Koh Samui and mainland Surat Thani sank at Don Sak pier after passengers and vehicles had left the vessel.
No one was injured, according to the Interior Ministry.
The ministry said that R10 ferry of Raja Ferry Co sank at a pier in mainland Don Sak district of Surat Thani at about 10am on Sunday.
Strong waves drove the ferry against the concrete pier, causing it to tilt and then sink to the seabed which was about four metres deep at that point.
No one was hurt because all passengers had already left the vessel, the ministry said.
The ministry ordered officials in southern provinces facing the Gulf of Thailand to keep all boats ashore during rough seas for public safety.
The port continued its services because other piers remained operational.