The C-130 American refueling plane fell in the northern Chuy province. No survivors have been found so far.
"The plane definitely belongs to the US transit center. On board were three crew members. Their fate is unknown," the emergency situations minister Kubatbek Boronov said in a televised comment after rushing to the scene.
"I cannot exclude that the three American pilots could have died, being burnt up alive in the explosion," he said, adding that the search operation would continue at least until nightfall.
The Manas airbase is a key to US military operations in Afghanistan, used to ferry troops into the country, refuel warplanes and evacuate wounded soldiers.
The US base said it was still confirming the report.