"For example, heavy rain in the Southern Alps could result in rapidly rising rivers in eastern parts, despite significantly dryer conditions away from the Alps."
Mr Kerr said there should be "brief respite from the rain and wind" later this week, probably late tomorrow and into Wednesday.
But a weather system moving across the country from west to east would probably bring strong winds to Auckland on Thursday as the Hutchwilco New Zealand Boat Show started in Greenlane.
Thunderstorms were expected in or around Auckland tomorrow morning.
WeatherWatch analysts said thunderstorms were possible between 8am and noon, with the city "on the edge of the risk zone - but certainly within it".
These thunderstorms would bring the risk of localised flash flooding and sudden downpours.
"Some also bring the risk of a damaging very localised wind gust," WeatherWatch said.
"As with any thunderstorm, there is the risk of cloud to ground lightning strikes and we strongly recommend that anyone who can hear thunder remain indoors until the storms pass."
WeatherWatch analysts did not expect serious problems for Auckland but would update their forecasts tomorrow.
They said a cold front tomorrow was connected to a big autumn low pressure system southwest of New Zealand.
The New Zealand Transport Agency (NZTA) urged drivers to take extra care on roads tonight and tomorrow morning, with a severe weather watch in place for the lower North Island.
"If the weather is looking particularly rough, we urge people to avoid or delay non-essential travel. It's much safer to stay put with a hot drink until it eases up," an NZTA spokesman said.
Strong wind and heavy rain were expected to make roads more treacherous.
Torrential rain was forecast during the morning rush hour on the Kapiti Coast and in Wellington.
NZTA said traffic would be heavy and visibility poor, so it was wise for motorists to allow extra time for travel, and if possible, to delay journeys.
"We saw how bad weather caused the motorways to clog up last week, and we're expecting more of the same in the morning."