Corporal Wassef Ali Hassoun failed to report for duty on Thursday, despite already facing a possible court martial on previous desertion charges.
In June 2004, the corporal disappeared from Falluja in Iraq for 19 days, before reappearing in Lebanon and saying he had been abducted by an Islamist group
A marines statement published at Camp Lejeune said Hassoun "was required to return by 12pm on 4 January, but has not yet reported for duty".
"As of 3pm today, his command officially declared him a deserter and issued authorisation for civil authorities to apprehend Hassoun and return him to military control," it added.
It was unclear why Hassoun was granted leave in light of the desertion charges against him. He faced the military equivalent of a grand jury investigation into his disappearance from Iraq and his subsequent reappearance.
The Article 32 investigation, which was to formally begin on 13 January, is supposed to decide whether the evidence against him warrants trial by court martial.
Hassoun, 24, enlisted in January 2002 and served as an Arabic language translator in Iraq when he disappeared from his camp in Falluja on 21 June 2004.
"I was captured and held against my will by anti-coalition forces for 19 days. This was a very difficult and challenging time for me"
Corporal Wassef Ali Hassoun
After a five month investigation by the Navy Criminal Investigative Services, the marines pressed charges of desertion, wrongful disposal of military property and two violations of larceny against Hassoun last month.
He was accused of theft of his 9-mm service pistol and theft of a government vehicle as well as desertion. On his return to the US in July, Hassoun denied reports that he had deserted his post.
"I was captured and held against my will by anti-coalition forces for 19 days," he said from the Quantico marine base near Washington.
"This was a very difficult and challenging time for me."