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Tom Phillips was charged with wasting police time after the events four months ago.
He did not show up to a court appearance at the Te Kūiti District Court on Wednesday and a warrant was issued for his arrest.
His lawyer Garth O'Brien told the court he had not heard from Phillips since he informed him of his court date.
Judge Phillip Crayton issued a warrant for his arrest.
Waikato West Police area commander Inspector Will Loughrin said Phillips is believed to be with his three children.
He would not say what police are doing to find him.
But Inspector Loughrin said they are receiving useful information from members of the public.
After the family's reappearance on September 30, police said they had been living in a tent in dense bush, inland from Kiritehere beach.