A total of 2,486 divers were involved in the record attempt off the coast of North Sulawesi, the Guinness adjudicator Lucia Sinigagliesi told AFP.
"This event was amazing and well-organised and made possible because of the people who came and participated," she said, after confirming that the group had broken the record for "Most People Scuba Diving Simultaneously".
The previous record was set in the Maldives in 2006, when 958 divers took part in a mass dive, she said.
The challenge was part of the Sail Bunaken 2009 maritime event being held as part of Indonesia's efforts to establish the Sulawesi town of Manado as a world-class tourist destination.
To mark Indonesia's 64th Independence Day, the participants unfurled the country's flag underwater.