Kayla Rosenfeld, the spokeswoman for Hawaii's Department of Human Services, said late Friday that the youth is "no longer in Hawaii."
Her brief emailed statement did not specify how or when Yahya Abdi left, whom he traveled with or where he went. A call to her office was not immediately answered early Saturday.
The boy's father, Abdilahi Yusuf, arrived in Hawaii this week from the family's home in Santa Clara, California, to bring him back.
Rosenfeld had said previously that the teen was in a Honolulu hospital after being transferred to state custody from the Maui airport, where he was questioned by FBI and airport officials following the April 20 flight.
Zahra Billoo of the Council on American-Islamic Relations in San Francisco, who has been speaking on behalf of the boy's family, declined to provide any details. "We're doing our best to help the family maintain the privacy they requested," she said Saturday morning.
Yahya Abdi withstood the flight from San Jose, California, to Maui after hopping an airport fence and climbing into the wheel well of a Boeing 767. He has not spoken publicly about the ordeal that raised questions about airport security and revealed the personal family drama of a Somali immigrant struggling to adjust to life in the United States.
Abdi, who lives in Santa Clara with his father, stepmother and siblings, had been unhappy in California and desperately missed his mother, according to those who know his family.
His mother lives in a refugee camp in eastern Ethiopia. Ubah Mohammed Abdule told The Associated Press that the boy longed to see her, but couldn't because his father told him she was dead and didn't allow contact.
The boy's sister, Najma Abdi, said Monday that their birth mother was lying, and that the father didn't take the children away from her or mistreat them.
A family spokesman didn't immediately return a call for comment early Saturday.
On Friday, the San Jose Mercury News reported that Mukhtar Guled, a cousin of the boy's stepmother, said it's not clear whether the father will be allowed to bring his son home.
"He could not see him. They won't let him see him or visit him or talk to him," Guled said.