Watada, however, said he admitted only that he did not go to Iraq with his unit, not that he had a duty to go.
In the 12-page stipulation of fact he signed last month, Watada acknowledged that he refused to deploy last June with his unit, the 3rd Brigade, 2nd Infantry Division, and that he made public statements criticising the Iraq war.
Watada agreed to the stipulation before the court-martial began in exchange for the government dropping two additional charges of conduct unbecoming an officer.
"As the order to take part in an illegal act is ultimately unlawful as well, I must as an officer of honour and integrity refuse that order"
"There is a material misunderstanding over what this stipulation is," said Head.
It was an unexpected end to a case that had rallied the anti-war movement in the first known court-martial of a US army officer for publicly refusing to serve in Iraq.
Army officials said the mistrial was an example of how the military justice system protects the rights of the accused.
Eric Seitz, Watada's lawyer, called it "significantly positive".
He said in a statement: "The mistrial is very likely to have the consequence of ending this case because double jeopardy may prevent the government from preceeding with a retrial."
The judge set the new trial to start on the week of March 19, but agreed the timing would be subject to change.
Watada will report for duty until the new trial begins.
Watada has said he refused to go to Iraq because he believes the war is illegal.
In a video statement in June, he said: "As the order to take part in an illegal act is ultimately unlawful as well, I must as an officer of honour and integrity refuse that order."