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Josh Malmo, 16, was cut on the hand by a flying shard of glass when the tree crashed into his room about 11.30pm. He was otherwise unhurt.
"He just needed a cup of tea with a couple of sugars in it," said his father, Andrew Malmo.
The 10m tree was brought down by high winds as the remnants of Tropical Cyclone Lusi passed over Auckland at the weekend.
It also flattened a caravan at the same property on Onewa Rd, Birkenhead, Mr Malmo said.
The noise of the tree coming down sounded like "the roof was being torn off the house".
"It also landed on my wife's caravan and pushed it right down to the ground," he said.
Mr Malmo said the family were waiting to hear from the landlord's insurance company. In the meantime, Josh was staying with a friend.
The storm, which was downgraded from a cyclone before it reached New Zealand on Friday night, brought down trees and caused damaging storm surges around the upper North Island.
It was last night expected to cause gale-force winds with gusts of up to 130km/h in Wellington, South Wairarapa and Marlborough, and heavy rain in parts of the South Island.
In Auckland, the storm caused surface flooding, power cuts and minor coastal erosion, said Civil Defence controller Clive Manley.
More than 10,000 homes lost power on Saturday, with up to 6000 customers out at one time, but Mr Manley said most were restored within a couple of hours.
Residents in 50 homes at northeastern beaches were told on Saturday night they might need to evacuate, as large swells threatened to inundate properties. But he said the swells subsided earlier than forecast, so there was no need to evacuate.
There was only minor erosion at North Auckland beaches, he said.
Three boats had to be secured in Auckland harbour on Saturday after breaking their moorings, and Fullers ferry sailings to Devonport were disrupted by the conditions.
The Fire Service northern communications centre received about 200 weather-related calls in Auckland, Northland, Waikato and Bay of Plenty from Friday evening to Sunday at 2pm, including 99 in Auckland.
In Northland, more than 30 businesses were inundated by sea water on Paihia's waterfront, and will be closed for a few days.
Part of State Highway 11 through central Paihia was closed on Saturday morning as high swells pushed sea water onto the road and into cafes and restaurants. Wind gusts reached 139km/h at Cape Reinga.
Auckland: Early low cloud, westerlies dying out, high 24C.
Hamilton: Morning showers, fine spells, high 24C.
Wellington: Severe gales before dawn, then strong northerlies, dying away tomorrow . High 21C.
Christchurch: Fine, late rain, developing northeasterlies. High 27C.
- additional reporting: Northern Advocate
- Heather McCracken of APNZ