Western Waikato Area Commander Inspector William Loughrin said Philips visited the property of a family member in the middle of the night.
"He advised them that he was safe and well and so were the children. He stayed there for a brief period, collected supplies and that's the last sightings of Tom."
Earlier this year, 34-year-old Phillips did not show up for a court date to face a charge connected to the earlier disappearance, with a judge subsequently issuing a warrant for his arrest.
Phillips' first appearance was originally scheduled for November but it was delayed due to Covid-19.
Loughrin said police believe the missing family is in the Marokopa area.
"While they are with their father who has been their primary caregiver for some time they have extended family who wants to and deserves to know where they are."
Phillips and his three young children went missing on September 11.
Since the family has been missing, Ember has turned 6 and Jayda will turn 9 next month.
When the family disappeared a second time, police confirmed they were making inquiries, but no search was launched and police said there were no immediate concerns for their safety.
Phillips has been described as a resilient man as well as an experienced bushman, fisherman and hunter.
It appeared the family stayed in a tent during their time in dense bush in September.
