The ministry said Kyrgyz search teams found the two fragmented bodies among the wreckage of the KC-135 Stratotanker aircraft on May 4.
The search continues for the third crew member.
Emergency Situations Minister Kubatbek Boronov said on May 3 that the black box from the plane had been found.
"The plane broke into five or six pieces. One of the engines was found and some 400 to 500 meters away another engine was found. The main body of the plane was split into two parts," Boronov told reporters.
Akjibek Beishebaeva, a spokeswoman for the U.S. transit center at the Manas airport near Bishkek, told RFE/RL: "The plane's crew is from the transit center outside Bishkek. The cause of the crash is under investigation."
The plane went down soon after departing the Manas airfield en route to Afghanistan.
Witnesses in the area of the village of Chaldovar, where the plane went down about 160 kilometers west of Manas, said the aircraft appeared to explode in midair and wreckage was spread over a wide area.
There were no casualties reported among local residents.
The U.S. military has been using the Manas airfield since December 2001 to support operations in Afghanistan.