The not guilty plea was entered at a hearing in Skagit County Superior Court in which Harris-Moore's lawyer, John Henry Browne, also accused the county prosecutor of misconduct in his handling of a press release about the charge.
Harris-Moore, who gained international notoriety after stealing planes, cars and boats during a two-year-crime spree, earlier acknowledged dozens of crimes and was sentenced to seven years in prison as part of a plea deal resolving charges against him in three Washington counties.
But Skagit County Prosecutor Rich Weyrich refused to take part in the plea deal, and had planned to charge Harris-Moore with second-degree burglary for breaking into Anacortes Airport and first-degree theft for taking a Cirrus plane there in 2010 and flying it to Orcas Island.
Weyrich said he didn't join the original plea deal because he wanted Harris-Moore to answer for the Skagit County crimes in a local courtroom.
However, Harris-Moore had already pleaded guilty to the theft of the Anacortes plane as part of his earlier plea deal, so he did not enter a response to that charge at Thursday's hearing. He pleaded not guilty to the single burglary charge.
Harris-Moore's lawyer Browne said last week it was "juvenile" for Weyrich to pursue further charges against his client, and the realization that Harris-Moore had already pleaded guilty to one of the latest charges made it "even more silly."
"Obviously Mr. Weyrich doesn't know the background of this case," Browne said earlier. "Maybe this will make him change his mind."
But in a statement issued Wednesday, Weyrich described the inclusion of the plane theft in the original plea deal as a deliberate attempt by the San Juan County prosecutor and Harris-Moore's attorneys to circumvent his authority.
"The sole purpose of this agreement was to circumvent my position that we would not be part of this plea deal which I felt was entirely too lenient," Weyrich wrote. "At no time was this office ever consulted or contacted about the case or informed that the defendant had been charged or pled guilty to a SKAGIT COUNTY charge in a county where it did not occur."
San Juan County Prosecutor Randall Gaylord said the fact that Harris-Moore landed the plane on Orcas Island, in San Juan County, gave him jurisdiction to charge the February 2010 plane theft. He said he and the other prosecutors involved in the plea discussions wanted to wrap as many charges as possible into the deal, both to bring the case to finality and to ensure restitution for as many victims as possible.
Browne said he expects the Skagit County theft charge to be dismissed because it violates his client's Fifth Amendment right not to be prosecuted twice for the same crime - double jeopardy, in legal parlance.
"Fifteen prosecutors from around the country, two U.S. attorneys and two judges agreed the sentence in this matter was appropriate," Browne said. "The only person who disagreed was Mr. Weyrich."
In court on Thursday, Browne also said the Skagit County Prosecutor's Office violated rules of professional conduct by asserting Harris-Moore is guilty in a press release.
Browne asked for a gag order on Prosecutor Weyrich, but the judge denied it because proper procedures for filing the request were not followed. Browne now says he will take his complaints against Weyrich to the Washington State Bar Association.
Harris-Moore is next scheduled to appear in Skagit County Superior Court on March 22, and a trial was set for April 29.
The youthful thief has been a thorn for Western Washington police since boyhood. He led authorities on a two-year game of cat-and-mouse in stolen cars, boats and airplanes. His run ended in 2010 after he crash-landed a stolen plane in the Bahamas and was arrested on a stolen boat in a hail of bullets.
He earned his nickname of "Barefoot Bandit" after his bare footprints were found at some crime scenes.