Col Sonny Leggett said: "While the cause of crash is under investigation, there are no indications the crash was caused by enemy fire."
The aircraft crashed in Deh Yak district, Ghazni province, an area with a strong Taliban presence.
It is unclear how many people were on board.
Col Leggett denied Taliban claims that additional aircraft had crashed.
Taliban social media accounts have posted unverified footage showing a burnt-out plane with US Air Force markings.
The video shows a Bombardier E-11A - the type of jet used by the US Air Force for electronic surveillance over Afghanistan.
Afghan authorities had initially said the crash plane belonged to state-owned airline Ariana, but the company quickly said all its planes were accounted for.