It seems the top of the country can't catch a break with more heavy rain set to drench the sodden region tomorrow.

As the storm-ravaged region begins a massive clean-up after the weekend's one-in-500-year flood that trapped people in waist-deep water, MetService meteorologist Andy Best said any hope of sun and fine weather would be short-lived.

"While there's some respite for Northland today unfortunately on Tuesday we're expecting more rain," he said.

And there was no immediate hope of the weather improving until Thursday.

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Northern highways that disappeared underwater at the weekend were now all open except a section of State Highway One through the Mangamuka Gorge which is blocked by an enormous slip.

The New Zealand Transport Agency said it was not expected to be cleared until later this week.

The highway connecting Kopu to Hikuai on the Coromandel Peninsula remains closed by two slips brought down during an earlier storm last week. It's hoped SH25A will be passable by the end of the day.

Flooding has also closed a stretch of State Highway 35 between Te Puia Springs and Tolaga Bay.

Meanwhile a fresh storm would be hitting the West Coast for the next 48 hours. MetService has issued heavy rain warnings and watches for Westland and Fiordland and the Canterbury and Otago headwaters with thunderstorms and intense rain set to lash the southern regions.

Best said with torrential rain falling over the next two days holidaymakers needed to be aware the region would be drenched by up to 180mm of rain in the coming 21 hours. Conditions would be particularly intense during thunderstorms hitting the region this afternoon.

"People should especially be aware of this especially if they are driving on the West Coast."

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