The U.S. military says in a statement the soldier acted in self-defense. AP quotes an statement released by the base's public affairs office as saying the U.S. serviceman "used deadly force in response to a threat at an entry control checkpoint."
The statement says the man was treated by U.S. military personnel and that he died of his wounds at the base's emergency hospital.
No further details were immediately available.
The Kyrgyz Foreign Ministry handed U.S. Ambassador Marie Yovanovitch a note in which it demands detailed information on the incident.
Kyrgyz media say the man was an ethnic Russian who was requesting permission to enter the base with his fuel truck.
The AKipress news agency quotes Kyrgyz investigators as saying the U.S. soldier shot at him twice after he exited his truck.
Acting Interior Minister Omurbek Subanaliev and other Kyrgyz officials traveled to the base, which is located some 30 kilometers from Bishkek, to investigate the incident.
The United States has been renting Manas air base from the Kyrgyz government since 2001 for operations in nearby Afghanistan.
(RFE/RL's Kyrgyz Service, AP, Kabar, AKIpress)