The secrets wound up with a suspected terrorism financier, FBI investigators say.
During an initial appearance Wednesday in U.S. District Court in Phoenix, Ariz., Hassan Abujihaad, 31, accepted removal to Connecticut.
He has been charged with supporting terrorism with intent to kill U.S. citizens and transmitting classified information, reports .
He apparently was working as a delivery man in Phoenix.
The investigation that began in Connecticut followed a suspected terrorist network across the country and into Europe and the Middle East.
Abujihaad, who also is known as Paul R. Hall, is charged in the same case as Babar Ahmad, a British computer specialist arrested in 2004 and accused of running Web sites to raise money for terrorism.
Ahmad is scheduled to be extradited to the U.S. to face trial.
During a search of Ahmad's computers, investigators said they discovered files containing classified information about the positions of U.S. Navy ships and discussing their susceptibility to attack.
Abujihaad, a former enlisted man, exchanged e-mails with Ahmad while on active duty on the USS Benfold, a guided-missile destroyer, in 2000 and 2001, according to an affidavit released Wednesday. He allegedly purchased videos promoting violent jihad, or holy war.
"In these e-mails, he supported Osama bin Laden and the attack on the USS Cole" in Yemen in 2000, said special agent Deb McCarley of the FBI's Phoenix office.
In those e-mails, Abujihaad discussed naval military briefings and praised those who attacked the USS Cole in 2000, according to the affidavit by FBI Agent David Dillon.
The documents retrieved from Ahmad show drawings of Navy battle groups and discuss upcoming missions. They also say the battle group could be attacked using small weapons such as rocket-propelled grenades. The ships were never attacked.
Authorities discovered Abujihaad's military e-mail address among the computer files, and he had a secret security clearance that would have allowed him access to that material, according to the affidavit.
The investigation was run out of Connecticut because Ahmad allegedly used an Internet service provider there to host one of his fundraising Web sites. Kevin O'Connor, the U.S. attorney for Connecticut, had no comment Wednesday night.
Ahmad was arrested in 2004 but the case against Abujihaad apparently received a boost in December following the arrest of Derrick Shareef, 22, of Genoa, Ill., near Chicago, who was accused of planning to use hand grenades to attack holiday shoppers at a mall.
According to the affidavit, Shareef and Abujihaad lived together in 2004 when Ahmad was arrested. After reading news reports of the case, Abujihaad became upset and said, "I think this is about me," Shareef told investigators.
Authorities then taped a phone conversation between Abujihaad and an informant in which Abujihaad appeared nervous. Though Abujihaad didn't say outright that he was involved in the leak of classified information, the affidavit provided enough evidence for an arrest warrant.
Abujihaad received an honorable discharge from the Navy in 2002, according to the affidavit.