The girl went missing on August 7 but was taken to the Darwin police station on Friday.
Detective Superintendent Kirsten Engels said officers were still trying to build a full picture of what happened over the past two weeks but were relishing in the fact the young girl was safely home.
She said it was believed the person who handed her over in Darwin was connected with the group that had taken responsibility for the alleged abduction.
"The investigators have been working tirelessly on this for the past 13 days. I would suggest some of them have not had much sleep or thought about anything more than getting (the girl) home," Supt Engels told reporters in Alice Springs.
"Their focus will now move to investigating who was involved in this and holding them responsible for their actions.
"Anyone involved in this alleged abduction and concealment, we will identify them and hold them responsible for what they've done."
Supt Engels said the girl had undergone a medical check and was in good health.
"I'm told that she's happy to be home. I certainly think she'll be happy to get back to the life that a five-year-old should be living," she said.
Earlier this week a special task force was established to find the missing girl, with their efforts focused on a group they said "continued to peddle ideologies and false information".
That came after a 50-year-old woman was charged over the alleged abduction.
She appeared in court in Darwin on Monday on one count of abducting a child under 16 and one count of attempting to abduct a child under 16.
Her case will return to court next week.
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