The Dornier 328 turboprop airplane operated by Express Air veered into a field Sunday shortly after touchdown, losing its landing gear and a propeller. Three crew members were also onboard.
Sutrisno said investigators were deployed to the airstrip in Boven Digul district, 2,300 miles east of capital Jakarta, to determine the cause.
Indonesia has 17,000 islands and relies heavily on air transport.
Hundreds of people have died in a series of crashes in recent years, prompting the European Union to ban all Indonesian airplanes.