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MetService duty forecaster Frances Russell said Lusi was crossing Marlborough at 9pm yesterday towards the Kaikoura coast and would track further east away from New Zealand early this morning.
The heavy rain in Otago should ''clear out'' but another weather front was approaching the South Island from the south and would bring more rain today, she said.
There were heavy rain warnings for Southern Westland between 10am and 10pm today.
''There will be rain in Otago and Southland but nowhere near the intensity they'll see on the West Coast.''
Dunedin fire service crews attended jobs related to flooding yesterday.
Staff from the Port Chalmers Fire Station were called to pump water from a flooded downstairs garage in Sawyers Bay and a Ravensbourne Fire Station crew helped re-secure a leaking iron roof in Maia.
Staff from St Kilda Fire Station assisted with a house that had flooded as a result of a blocked drain in St Kilda.
Dunedin i-Site manager Louise van de Vlierd said bad weather forced cruise ship Sun Princess to bypass Dunedin yesterday.
However, Celebrity Solstice berthed at Port Chalmers and many of the more than 3000 passengers and crew braved the bad weather to visit Dunedin, she said.
Voyager of the Seas was expected to berth at 7am today, she said.
Winds were picking up in Wellington last night and heavy rain was falling in the Nelson ranges. Gusts of up to 130kmh were expected in Wellington overnight and severe weather warnings were in place for gales and heavy rain in parts of the South Island and lower North Island.
In the north, the cleanup began yesterday after the storm brought winds of up to 140kmh at Cape Reinga and high swells along the east coast.
Northland's regional harbourmaster reported several boats had come ashore at Houhora, Mangonui and Paihia.
State Highway 11 was closed on Saturday night as strong winds swept high tides across a section of the highway between Kawakawa and Paihia.
Strong easterly winds gusting to 120kmh blew a shed through power lines at Whangarei Heads overnight on Saturday, cutting power to 2000 homes, a Northpower spokesman said.
In Auckland, the storm caused surface flooding, power cuts and minor coastal erosion, Civil Defence controller Clive Manley said.
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.
Josh Malmo (16), of Birkenhead, 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.
Additional reporting APNZ.