Yee's lawyers, in an appeal filed late on Sunday, said Army Major General Geoffrey Miller's 22 March decision to put a written reprimand in Yee's permanent military record should be set aside as "unjust and disproportionate" and "a grave miscarriage of justice," and the charges against Yee dismissed.
Miller commanded the prison facilities at the US naval base at Guantanamo Bay, Cuba, where Yee, 36, ministered for 10 months to foreign detainees. Miller left the post two days after deciding Yee's case.
Army General James Hill, who heads Miami-based US Southern Command and is responsible for Guantanamo operations, normally would decide the appeal. But Yee's lawyers asked Hill to excuse himself in light of his prior involvement in the case.
Yee's legal team, headed by Eugene Fidell, said Miller also was not impartial.
"His insistence on retaining the case regardless of the truncation of Chaplain Yee's rights confirms his inability to bring to bear the requisite impartiality," they said.
"The proceeding that ensued is a hoax by any standard."
The appeal faulted Miller for giving Yee only three days' notice of a nonjudicial punishment hearing after dismissing all criminal charges against him, depriving the defence of time to prepare a case.
It said the army gave Yee's lawyers the evidence it planned to use just 11 minutes before the start of the hearing, and accused Miller of improperly consulting in private with an army prosecutor during the proceedings.
The chaplain ministered to
detainees at Camp X-Ray in Cuba
In the administrative hearing last week, Miller found Yee guilty of committing adultery and downloading pornography on a government computer, but the decision did not represent a criminal conviction under military law.
Miller only three days earlier dismissed all six criminal charges against Yee, including mishandling classified information and the lesser adultery and pornography charges.
This marked the collapse of the army's espionage case against Yee that began with accusations in court documents of spying, mutiny, sedition, aiding the enemy and espionage.
The appeal said Yee already has been severely punished since his arrest last September, noting he spent 76 days in solitary confinement at a Navy brig in South Carolina.