Staff Sergeant Camilo Mejia reported himself to the Florida National Guard on Tuesday in preparation for seeking conscientious objector status, and repeated his determination not to return to the Middle East.
"I'm prepared to go to prison because I'll have a clear conscience. This is an oil-driven war, and I don't think any soldier signs up to fight for oil."
But National Guard officials said they would consider the non-commissioned officer a deserter.
Mejia said he was distraught over an incident in Iraq in which he and others had been ambushed.
As his unit returned fire, terrified innocent civilians panicked and ran into his unit's line of fire. He has not given any estimate to the number killed, but it had led him to apply for conscientious objector status.
The 28-year-old was in Iraq for about five months until October, when he returned home on leave.
Florida National Guard spokesman Jon Myatt said Mejia had been classified as a deserter because he was missing from his unit for more than 30 days.
Myatt said a warrant to arrest Mejia as a deserter could be issued if Mejia failed to appear on Wednesday at Fort Stewart where his unit - the 1st Battalion, 124th Infantry Regiment - was deployed from.
He would not discuss the potential penalties that Mejia could face, and a spokesman at Fort Stewart did not immediately return a call seeking comment.
Not a coward
Mejia was accompanied to the armoury by his mother, an aunt and private Oliver Perez, who served with him.
Perez said Mejia was "a brave leader'" and should not be prosecuted. "I fought next to him in many battles. He is not a coward."
"I'm prepared to go to prison because I'll have a clear conscience. This is an oil-driven war, and I don't think any soldier signs up to fight for oil"
Staff Sergeant, 1st Battalion 124th Infantry Regiment
A native of Nicaragua, the sergeant is a permanent resident of the US who served in the army for three years.
More conscientious objectors
In Iraq, a commander said two US army medics had applied for conscientious objector status.
Captain Todd Grissom said the two, both privates first class, notified the army of their request on 9 February.
The two want to be honourably discharged from the military because the idea of killing is "revolting" to them, Grissom said on Tuesday.