The group of six, identified as five Italians and a Belgian, had headed out to Sangalaki island, a popular dive spot in the Derewan Islands chain in East Kalimantan province, on Saturday, provincial search and rescue chief Hendra Sudirman told AFP.
"Two Italians among them who went snorkelling were safe. But four others, comprising of three Italians and a Belgian, who went diving were reported missing Saturday evening," he said.
"We have sent out rescue boats to look for them in the water as well as comb the beaches and surrounding areas but so far, we have found no trace of them," he said.
"The currents are strong and waves are up to 2.5 metres. We hope they have drifted to the smaller islands and are safe," he added.
Sudirman said the authorities are still investigating the case and searching for the missing tourists would be a priority.
State news agency Antara reported that a local guide accompanying the divers has been found safe and is being treated at a hospital.
Indonesia is a popular scuba diving destination in Asia but accidents have been reported in recent years.
Two of seven Japanese divers were killed in a diving trip off the resort island of Bali in February last year.