According to Marine Capt. Charles Palmer of the 1st Marine Logistics Group at Camp Pendleton, the Marine was questioned by the Naval Criminal Investigative Service - the federal agency in charge of investigating Navy and Marine Corps criminal cases - and was released to his command pending further investigation.
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"This command takes this matter and all allegations very seriously," said Palmer. "The incident is under investigation, and we will continue to cooperate with NCIS and appropriate authorities."
It was unclear how the girl and the Marine came into contact before military police found her in the barracks during the daytime on June 28, Palmer said.
According to the San Diego Sheriff's Department, her grandmother reported her missing on June 13 and told authorities she had run away from home four days earlier. The grandmother told the deputy who interviewed her that the girl had run away before but only for brief periods.
The teen's information was entered into multiple missing person databases, including the National Center for Missing and Exploited Children, the sheriff's department said.
After she was found on base, authorities returned the girl to her grandmother, according to the sheriff's department.
Military officials say they could not release any other details, including the age or rank of the Marine. The case has been handed over to the NCIS.
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NCIS spokesman Jeff Houston said no one has been arrested or charged in the case, according to ABC News. The sheriff's department and the San Diego Human Trafficking Task Force are assisting the investigation.
Meanwhile, the girl's aunt, Casaundra Perez, posted a video to TikTok in which she said that her family was afraid of retaliation from the military and from the man she believes trafficked her niece.
"I will not rest until the whole world knows and those responsible are held accountable and justice is served," said Perez in a video.
"Out of respect for the investigative process, NCIS does not comment on, confirm details relating to, or confirm the existence of ongoing investigations,'' the agency said in a recent statement.
ABC News contributed to this report.