The damaging wind funnel struck Awatuna, north of Hokitika, just before 6am.
There are unconfirmed reports of a building losing its roof and other damage to property.
A police spokeswoman said the tornado destroyed railway crossing bells on Old Christchurch Rd at Awatuna.
"A mini tornado came through the area and took out crossing bells and road signs," she said.
A Fire and Emergency spokesman said firefighters had not been called.
There are reports a building has lost its roof after a tornado roared through Arahura Pa, north of Hokitika.
Wild weather has also hit the North Island, where 30 lightning strikes have hit land.
Three houses have been struck by lightning on the Manukau Heads and a Doc building is ablaze as thunderstorms cause problems across the North Island this morning.
Two people had to be rescued from their parked vehicle after becoming trapped by rising floodwaters at a Waitomo reserve.
Fire and Emergency northern shift manager Jaron Phillips said the Department of Conservation's Pureora Forest Park office on Barryville Rd was engulfed by fire.
A fierce thunderstorm was over the Waitomo District at the time and a lightning strike may have sparked the blaze.
"There was a front moving across and there was a large storm at the time," Mr Phillips said.
Fire crews from Mangakino, Benneydale, Tokoroa and Otorohanga were battling the blaze in the single-storey building.
Meanwhile, at Manukau Heads, three neighbouring houses had been struck by a bolt. Four fire crews were headed to the remote west coast properties.
The Fire Service said they were called to three properties on Kohekohe-Karioitahi Rd in Waiuku about 5.30am. The roof of one house was badly damaged.
"One property, as a result of being struck by lightning, had damage to the roof - which resulted in a water leak, so the brigade assisted there," a spokesman said. "The second property had smoke showing from power sockets and lighting fixtures and the third property had minor flooding."
The settlement of Mangakino had also been lashed by stormy weather. Flooding and a lightning strike hit the main telephone network before dawn.
Mr Phillips said fire crews encountered flooding leaving to fight the Pureora blaze.
A strike had triggered the fire alarm at the Mangakino Telephone Exchange and the town was now without landlines, he said.
Meanwhile, a pair spending the night in their vehicle at the Ruakuri Reserve awoke to find water coursing through their parked vehicle.
A police spokesman said firefighters walked the pair to safety through the fast-rising floodwaters that had swamped the scenic reserve's car park.
MetService forecaster Tom Adams said the band of thunderstorms would cross Auckland this morning.
So far there had been 30 lightning strikes on land.
The storms would give way to showery weather and fresh thunderstorms would hit later in the day, he said.
