Authorities in Papua New Guinea have called off the search for an Australian man and his two colleagues who went missing after their boat capsized near the capital Port Moresby.

PNG's National Maritime Safety Authority (NMSA) said the search was called off after receiving advice from an Australian expert that the time frame for survival would have expired by last light on Monday.

The three missing men were part of a group of four who were headed towards an island 30 minutes south-west of Port Moresby on Saturday.

One man was rescued by helicopter one day after the incident, after he swam to nearby Idihi Island, about 30 kilometres from Royal Papua Yacht Club, where the boat had been moored.

Map Points of interest in the search for a boat missing off the PNG coast

He told authorities their boat had overturned in rough seas.

The men were employees at accounting firm KPMG in Port Moresby.

A statement from the company confirmed the boat the men had been in was found, but it said hope of finding any survivors was fading.

NMDA general manager Paul Unas warned boat owners to exercise sea safety, especially during windy periods.