The Cessna aircraft failed to return from a surveying mission in Bontang, Temindung Airport chief official Rajoki Aritonang said on Friday evening.
It was chartered by Elliott Geophysics International, a Perth-based surveying company.
Australia's Department of Foreign Affairs and Trade (DFAT) said it was aware of a plane missing in Samarinda, in the East Kalimantan province.
"We understand an Australian citizen was on board," a spokesman told AAP.
Aritonang said the plane left Samarinda, the provincial capital of East Kalimantan, on Friday morning for a 90-minute flight to survey a coalmining site.
It was carrying the pilot, two other Indonesians and the company's Australian owner.
National Search and Rescue Agency spokesman Gagah Prakoso said an eight-member team was sent to search the area where the plane lost radio contact with the airport.
The DFAT spokesman said a search and rescue operation was cancelled because of poor light and was likely to resume in the morning.
The Australian embassy in Jakarta is providing consular assistance.
