Search and rescue teams were heading to the area, said Bambang Ervan, a spokesman for the Ministry of Transportation. Bad weather, however, forced at least two helicopters to turn back.
The Sukhoi Superjet-100, a civilian plane, took off from Jakarta's Halim Perdanakusuma Airport at 2 p.m. (0700 GMT) and was scheduled to return 50 minutes later.
Air controllers lost contact after it reportedly dropped from 10,000 feet to 6,000 feet near the Salak mountains in West Java, said Gagah Prakoso, a spokesman for the national search agency.
Several diplomats from the Russian Embassy, representatives from airline companies and journalists were among the 46 on board, said Rear Marshal Daryatmo, another search and rescue official.
The plane, developed by the Russian aerospace company Sukhoi in co-operation with Western partners, is the first completely new airliner designed by Russia since the Soviet collapse.
It was on a "Welcome Asia!" road show with stops in countries stretching from Pakistan to Laos and Vietnam.
Russia has hoped that the short- to mid-range jet, which made its maiden run in 2008, will help it break into international markets dominated by Boeing and Airbus.