Michael Lyons says he became a conscientious objector to the war after reading of the "enormous underreporting of civilian casualties in the conflict" in leaked military documents published by the secret-spilling website, the Associated Press reports.
Lyons original request had been rejected by his commanding officer, and his appeal was before the Advisory Committee on Conscientious Objectors.
The committee had heard how anecdotal evidence of civilian casualties, including children, had prompted Mr Lyons to research the political reasons for the war, reports the U.K. Telegraph newspaper.
Special Report: WikiLeaks
"I was unable to find a real, just and noble cause to go out but I still had a sense of duty to my country," he said.
Lyons, 24, joined the Navy in 2005 and was due to serve in Afghanistan next Aprilthe AP reports.
His appeal against that decision was rejected Friday in London, the AP reports. The judge said he would give his reasons for the decision later.
Asked if he was scared of going to Afghanistan, the Telegraph reports Mr Lyons as saying: "I had the normal fears of leaving my wife a widow and fears of seeing things or being injured but I wouldn't say anything more than anyone else required to go out there."
He broke down in tears as he told the hearing: "If more people in my position stood up, there would be a lot less innocent lives lost around the world."