The MetService has described the weather as "not a great-looking day for royal visitors" as it puts the central part of the country under severe weather watch.
MetService meteorologist Dan Corbett said the heaviest rain was in Hawke's Bay and Gisborne - which had severe weather warnings.
People in those areas were advised that heavy rain could cause rivers to rise rapidly, with surface flooding and slips possible. Driving conditions would also be hazardous with poor visibility likely, the MetService warned.
Up to 100mm of rain may accumulate in the coastal hills and ranges of Hawke's Bay in the 12 hours to 9pm. In Gisborne, between 70 and 100mm of rain could accumulate by tonight.
A severe weather watch - one notch down from a warning - was in place for Wairarapa, Wellington, and Marlborough.
''It's not a great-looking day for royal visitors,'' MetService meteorologist Dan Corbett said.
The thunderstorms, which were expected to be isolated, were the result of a combination of moist air, onshore winds and daytime heating over the land.
The low pressure system bringing the rain was expected to remain slow moving over the northeast of the North Island today and tomorrow, when it should weaken, MetService said.
Heavy rain was also expected today in the rest of Gisborne, the coastal hills and ranges of Wairarapa and the Rimutaka Forest Park including the Orongorongo ranges of southeast Wellington. In the South Island heavy rain is expected in the Kaikoura ranges.
The rain was expected to lessen tomorrow, with Thursday and Friday forecast to be the driest days of the week.
The far northwest and far south of the country were expected to stay mainly dry today, but chances for rain would improve in the coming days as further lows moved towards the country from the west, MetService said.