Captain James Yee, a 35-year-old Chinese-American who converted to Islam in the 1990s, has been in custody since 10 September.
Southern Command spokesman Captain Thomas Crosson declined to comment on the reasons for Yee’s arrest.
"There is an ongoing investigation, and no charges have been filed against Captain Yee," he said. "I don't know where in the judicial process he is."
But another US government official, told French news agency, AFP that the main suspicion was espionage.
An unconfirmed report carried by BBC World said the FBI had found classified documents on Yee and a map showing the holding locations of the Guantanamo detainees.
On Saturday, Yee, who changed his first name to Yusuf after converting to Islam, was being questioned at the US Navy detention facility in Charleston, South Carolina, the same institution where suspected al-Qaida operative Jose Padilla and Yasir Isaam Hambi have been held.
In his military training, Yee specialised in artillery defence and was a Patriot missile fire control officer.
He later moved to Syria where he taught English, and received Arabic lessons and religious training. Yee later returned to the US military as a Muslim chaplain.
After the 11 September attacks, Yee became a known figure on the media circuit giving interviews about the peaceful nature of Islam and condemned the New York and Washington strikes.
Yee was assigned to the prisoner camp at Guantanamo Bay in November 2002 to serve as both religious counsel to the approximately 650 inmates held there and an adviser to US base commanders on Muslim affairs.
Since the attacks extremist neoconservative and Zionist voices such as Daniel Pipes have called for greater scrutiny of Muslims holding official positions including chaplaincy posts in the military.
Most of the Guantanamo prisoners, who come from more than 40 countries, were captured by US forces in Afghanistan and include, according to US officials, hardline al-Qaeda and Taliban militants.
They are being held at the base as enemy combatants not entitled to the same legal protections granted US citizens. Human rights organisations have condemned their treatment as a violation of international law.
Some of the inmates are expected to face military tribunals being set up by the Pentagon.