Residents in the Hobonsville suburb of New Zealand's largest city were urged to seek shelter in their homes as authorities feared additional twisters could follow the first one, which struck just after noon, stuff.co.nz reported.
The deaths reportedly occurred near a construction site west of Auckland. At least seven more people were injured.
The area, hit by severe weather, was forecast to receive more thunderstorms.
The killer tornado also uprooted trees and tore roofs off homes, the report said. Numerous power lines were downed, hampering search efforts in buildings and flooding also was reported, emergency crews said.
One construction worker was quoted as telling Radio New Zealand at least two people may be missing.
The New Zealand Transport Agency said State Highway 18, the upper harbor motorway, remained closed between Brigham Creek Road and Greenhithe Road due to debris on the road, Stuff reported.
Describing the tornado, local administrator Toni Hayward said: "It came right through here and picked stuff up and threw it on the road. The sky went all dark and there was a big clap of thunder, all the trees were flattened."
A spokeswoman for Prime Minister John Key said emergency crews were at the scene and residents were being advised to remain indoors.
The New Zealand Herald said about 20 to 30 tornadoes touch down in New Zealand annually, but fatalities are rare.
Meteorologists said tornadoes in New Zealand are a cold season phenomenon, unlike those in the United States, which occur mostly during the warm months.
The Herald reported New Zealand's worst tornado was in August 1948, when three people were killed, 80 injured and about 150 buildings destroyed in Hamilton.