Gusts up to 120km/h are possible for Wellington and Wairarapa, which are both under a wind warning, Flynn said.
Further north, Auckland is expected to enjoy temperatures of up to 23C, but showers are set to dampen plans for those hoping to enjoy the first day of 2017 outdoors all day.
Buller is under a heavy rain warning until early afternoon, while there will be watches for heavy rain in northern Fiordland and the headwaters of Canterbury's lakes and rivers.
Meanwhile inland Canterbury may be getting severe gales until early afternoon on Sunday. Wind is also expected to strengthen in Marlborough.
The tourist mecca of Queenstown looks like being one of the best places in the country to enjoy January 1. Fine weather is forecast all day.
Weather for the first week of 2017 in general is expected to be a mixed bag.
Monday will see the North Island experiencing scattered rain and showers south of Auckland, but Auckland and further north should be "mostly dry".
Temperatures are also set to be high on Monday, with Kaikoura at a high of 30C, Ashburton, Timaru, Napier and Hastings getting highs of 29C, and Auckland sitting in the mid to high 20s.
Wellington will be missing out on the fun, with temperatures expected to stay in the high teens, though the Hutt Valley may see some in the 20s, Flynn said.
The front bringing the rain will be "slowing down and very gradually tracking its way across the North Island".
Parts of the South Island may be getting some rain, which will "briefly" become heavy for Buller and Nelson.
The low which is bringing the unfestive weather is expected to clear on Wednesday.