The charges related to disclosure a US Navy battle group movements as it traveled from California to the Gulf in 2001, prosecutors said in a news release.
The suspected disclosures occurred just months after an attack by suicide bombers on the USS Cole during a refueling stop in Yemen in October 2000, which killed 17 sailors and injured dozens more.
If convicted on both charges, Abujihaad faces a maximum term of 25 years in jail.
Websites in Connecticut
The charges were brought in Connecticut because the Azzam Publications websites were hosted for a time on servers in the state.
The complaint alleged that Abujihaad sent several e-mails to members of Azzam while he was on active duty in the Middle East and stationed aboard the USS Benfold, a ship in the battle group whose movements were disclosed.
The emails were recovered in a December 2003 search by British police of the London home of Babar Ahmad, a British national linked to Azzam.
Aside from details of the warships' movements, a document Abujihaad is accused of leaking went on to discuss the group's perceived vulnerability to terrorist attack, prosecutors said.
Abujihaad was discharged from active duty from the United States Navy in January 2002, authorities said.