A three-year-old boy who died after going missing from a remote NT community was Killed by dogs, according to Police.

The boy went missing on New Year's Eve, with police believing he wandered off and got lost.

The boy's family with the help of police searched for hours until he was found outside Hermannsburg at 9am the next morning.

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He was rushed to a local health clinic but died there.

Police believe he was killed by camp dogs, animals that hang around the community but are not fully domesticated.

Two dogs have been held for forensic testing.

Assistant Commissioner Sachim Sharma said police were not yet ruling out foul play.

"When there is no information that there is no foul play, we will always investigate to the nth degree," he said yesterday.

A report will be prepared for the coroner.

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"Anyone in that situation would be distraught," Mr Sharma said.

"We all have kids and if you don't you will know a family that has kids.

"That is a horrible, horrible situation to be in."

Hermannsburg, or Ntaria, is a largely Aboriginal community about an hour away from Alice Springs.