Before the pair was found Pitkethley said in a media statement police were extremely concerned for the toddler's safety.
Police had issued an alert for Barlow and urged him to hand himself in.
"This is an unfolding incident with a number of staff actively working to locate Barlow. We have extreme concerns for the safety of the toddler and are working hard to ensure the pair are found," the detective said.
The 36-year-old was last seen leaving the Ngati Maru Highway address in a 2001 white Toyota Corolla.
Police officers remained at the Ngati Maru Highway scene working to establish exactly what had happened, he said.
The house involved is understood to be near the old abattoir, on the southern entrance to the Coromandel Peninsula town.
Neighbours reported seeing emergency services at the scene, but knew little more.