Former U.S. Army Sgt. Charles Robert Jenkins, who arrived in Tokyo July 18, is accused of deserting to North Korea in 1965.
"He faces serious charges, including desertion," State Department spokesman Richard Boucher said.
In a written statement, Boucher said U.S. military doctors have been in contact with Japanese doctors treating Jenkins.
The spokesman, however, refused to discuss legal implications of the case.
Jenkins, 64, married a Japanese woman while living in North Korea where the couple also had two daughters.
A government spokesman in Tokyo told reporters last week Jenkins wants to speak to a U.S. military lawyer. But the move did not necessarily mean Jenkins was ready to plead guilty and seek a plea bargain, he added.
Instead of deporting Jenkins for trial in the United States, Japan is seeking a compromise to end the issue.
Jenkins met his wife after she was abducted by North Korean agents in 1978. She returned to Japan in 2002, but had to leave her husband and two daughters behind.