A Spanish family of four is missing after a tourist boat sank in rough seas in Indonesia, state news agency Antara reported on Saturday.

The vessel was carrying 11 people when it sank in the Padar Island Strait near the popular destination of Labuan Bajo on Friday night, Antara said.

Seven people, including two Spanish tourists, four crew members and a tour guide, were rescued.

A search for the remaining four was continuing on Saturday, with Padar Island closed to tourists due to extreme weather conditions.

The Labuan Bajo port authority attributed the sinking to high waves of up to three metres, Antara said.

"This made it difficult for us to carry out the initial search," port authority chief Stephanus Risdiyanto told the agency.

Marine accidents occur regularly in Indonesia, a Southeast Asian archipelago of around 17,000 islands, often due to lax safety standards and bad weather. (AFP)