"We're focusing our search on the border between Kerom and Pegunungan Bintang istricts... it's a mountainous, jungly region," Suwandi Miharja, the air force commander overseeing the search, told the AFP news agency.
"They're flying beneath the clouds. The weather is unfriendly... foggy and rainy."
Ground controllers lost contact with the plane as it flew over densely forested and mountainous area.
Indonesia has suffered a series of air disasters in recent years, affecting both its commercial and military aircraft.
Last month, the European Union removed four Indonesian airlines - flag carrier Garuda Indonesia, Mandala, Airfast and Premiair - off its blacklist of banned carriers, citing safety improvements.
However, the ban remains in place for all other Indonesian airlines.
Air travel is one of the few options for long-distance travel in sparsely-populated Papua and accidents are relatively common.
In the past some aircraft thought to have crashed in the region's dense jungle have never been found.