A snorkeling boat carrying 13 people, including 11 Australian tourists, capsized in rough seas off Bali on Friday, killing a woman and injuring two others, police said.

The Sea Dragon boat was on its way from a port in Bali to Nusa Penida, a popular tiny island near Bali, when it was overwhelmed by high waves, local police spokesperson Agus Widiono said.

The group was looking at underwater scenery when their boat was hit by a large wave that threw a 39-year-old woman, identified by police as Anna Maree, overboard.

Passengers sit on a boat carrying tourists including a number of Australians that capsized in the waters off Nusa Penida Island, in Bali.
Passengers sit on a boat carrying tourists including a number of Australians that capsized in the waters off Nusa Penida Island, in Bali. (Klungkung District Police)

It was followed by a second wave that capsized the boat in Kelingking waters, Widiono said.

A nearby boat was rushed to rescue 12 survivors, including two local crews and two injured tourists from the choppy waters.

Rescuers also found the body of Maree, the spokesperson said.

Survivors were treated at nearby health clinic and are in stable condition.

Maritime accidents have killed hundreds of people in Indonesia in recent years. Boats are often overcrowded, and safety regulations are poorly enforced.

The vast archipelago country spans more than 17,000 islands with a population of 280 million, and boats are a popular and relatively cheap form of transportation.

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