Air Force spokesman Larry Clavette said that one charge of espionage against Senior Airman Ahmad al-Halabi, 23, was dropped, as well as an allegation that he aided the enemy and wrongfully e-mailed detainee information.
But he added: "A number of very significant charges remain referred against him. The government fully intends to prosecute."
Al-Halabi, who is of Syrian descent, has denied the charges. He worked as a translator at Guantanamo for nine months.
A resident of Detroit, Michigan, al-Halabi was arrested on 23 July and accused of carrying jail maps, letters and other sensitive documents away from Guantanamo, where suspected al-Qaida and Taliban members have been detained.
Charges still pending against al-Halabi include espionage, failure to obey an order, retaining documents without authority, making false official statements and executing a fraudulent credit application scheme.
The spokesman said it would be "inappropriate" to discuss the specific reasons for the three dropped charges .
Al-Halabi is expected to go on trial at the Travis Air Force Base in northern California next year.
He is one of four men, including another Arabic translator and a Muslim chaplain, charged in connection with their work at Guantanamo.