Their mother - who was at work - arrived shortly after authorities did.
Their father said he was shocked when he got a call from his wife that he needed to get home as there had been a fire.
"We're not reckless parents," he told One News. "We could've been coming home and having two less kids."
He said he and his wife left early for work every day and had expected his daughters to be taken to school.
Fire safety investigators have yet to determine the cause of the blaze, which is thought to have started in a bedroom at the back of the house. A 68-year-old man, understood to be the owner of the property, is due to appear in the Manukau District Court.
He has been charged with leaving a child under the age of 14 without reasonable supervision.