The motion filed late Friday seeks the dismissal of the first-degree murder charge stemming from the death of the boy's father, 29-year-old Vincent Romero. The boy is also charged with first-degree murder in the death of 39-year-old Tim Romans, Romero's roommate.
The motion explicitly allows the refiling of the charge if it is granted.
The prosecutor's office wouldn't explain its actions. The boy's defense attorney, Benjamin Brewer, declined to comment Friday, citing a gag order in the case.
Police in the small eastern Arizona town of St. Johns allege that the boy killed both men with a .22-caliber rifle in their home on Nov. 5.
A well-known Arizona defense lawyer not involved in the case said there could be many reasons why a charge would be dismissed.
"There's some reason legally or factually that they don't want to proceed with that murder at this time - and that normally means there's something they need to investigate further - the case is not ready to proceed," Tucson attorney Mike Piccarreta said.
Romero and Romans were found dead Nov. 5.
Police say the boy confessed to the killings. But he gave conflicting accounts of the shootings in an hourlong video of his interview with authorities in St. Johns.
A 12-minute segment of the video was posted Nov. 17 on Phoenix television station KTVK's Web site. The station said it got the video from the prosecutor's office in Apache County, where the shootings occurred.
But a legal analyst on CBS' The Early Show Thursday called the police interrogation "absurd."
"What we know is that children under 12 are especially susceptible to questioning by an adult," legal analyst Lisa Bloom said.
"I think I shot my dad because he was suffering, I think," the boy said toward the end of the hour-long interrogation, though Bloom notes that the admission comes only after repeated officer questioning.
"Children tell authority figures what they think the authority figure wants to hear," said Bloom. "This child was not Mirandized; there was no attorney for him in that room; there was no parent or legal guardian. He was simply answering questions by two police officers in uniforms with guns."
A defense attorney, Benjamin Brewer, has said police overreached in their questioning of the boy, who was not represented by a family member or lawyer during the interview.
On Wednesday, a judge ruled that the boy will be allowed to spend the Thanksgiving holiday next week with his mother, a move that drew criticism from the family of the second victim.
St. Johns police Chief Roy Melnick has said he would push for the boy to be tried as an adult, though some analysts think even a juvenile court trial would be too much.
"Children this age believe in the tooth fairy, they believe in magic … it's absurd," said Bloom. "This child should not be in juvenile court or adult court, in my opinion. He should be a ward of the family court and get some social service attention."
Authorities and the defense attorneys have been unable to answer questions about the case since the court issued a gag order.
A status conference in the case has been scheduled for Dec. 8.