The refuelling plane exploded in mid air when its cargo of fuel ignited on its way to Afghanistan on Friday, accident investigators said.
Experts were still trying to work out what led up to the crash, said Kuvan Mamakeev, the Kyrgyz state prosecutor responsible for investigating transport crimes and accidents.
"It could be because of the fuel, because of the engine, the weather conditions or the human factor," he told Reuters.
Remains of the two bodies were found on Saturday, and a third person on board was still unaccounted for, Kyrgyzstan's Minister of Emergency Situations, Kubatbek Boronov, added.
The Boeing KC-135 Stratotanker took off from the US military transit centre at Kyrgyzstan's Manas airport, which US forces maintain for operations in Afghanistan, with around 70 tonnes of fuel on board, a local ministry official said.
The wreckage of the plane was scattered over a 4 to 5 km area in a mountainous area near the Kyrgyz village of Chaldovar, the official added.