"Another concerning factor is that the heaviest rain may once again hit the same regions affected by flooding this week."
The new low was not a "carbon copy" of the current system, but the regions hit by flooding this week would be most exposed to heavy rain.
Mr Duncan said Waikato and Coromandel waterways still dealing with significant flood runoff would be especially under pressure.
The new low could also last longer, which meant some regions could see heavy rain for a day of two before being hit by more downpours as it slowly churned by.
WeatherWatch said it was not forecasting solid rain, but there was a high risk of rain at some point every day, with some days much wetter than others.
Northern and western parts of the North Island were likely to be most exposed, but the heavy rain could also swing back around into the east, as it did this week.
The western, northern and eastern coastlines of the South Island could also be exposed to heavy rain.
Some regions could be fairly sheltered, but further updates were needed before it was known exactly where the rain would fall.
Mr Duncan said it was too soon to predict the amount of rainfall, but even a low-end rain warning could cause more flooding and slips with the ground so saturated.
Waikato Regional Council emergency management officer Greg Ryan said the council was today keeping a close eye on the Piako and Waitoa rivers, which remained heavily swollen as peak levels moved through.
Emergency ponding zones in paddocks near the Piako River could take on water over the next two days as part of the Piako flood management scheme, which takes pressure off land beside the lower Piako.
"Our flood management infrastructure is coping well and is expected to help prevent any significant damage to property. But we will be monitoring the situation carefully.
"We will have people out on the ground regularly checking stopbanks and flood pumps."
The Ohinemuri and Waihou rivers have begun to recede and are forecast to steadily decline in coming days.
Further west, the lower Waikato River was expected to remain heavily swollen for the rest of the week, especially around Mercer.
River levels were also elevated at Hamilton but were expected to slowly recede in the coming days.
The swollen rivers have caused headaches for Waikato farmers, including a flood-stranded man who had to be lifted to safety by helicopter yesterday after he was forced to shelter in a barn overnight.
The 59-year-old man was feeding stock on his farm south of Te Aroha when he was caught out by the rising Waihou River, which flooded the back paddocks bordering the river.
The Westpac Waikato Air Ambulance crew picked up the farmer "in good spirits and health" yesterday morning.
He was dropped off at his farmhouse and, after a quick meal, he got straight back to work rescuing cows.
Highways closed by flooding and slips reopened yesterday, but work was still continuing to clear the remaining debris today.
Motorists should expect delays on State Highway 2 at the Athenree and Karangahake gorges, where both lanes were open but clean-up work was ongoing.
There could also be delays on SH1 south of Cambridge, SH35 on the East Cape and SH25 in Coromandel, where slips had caused lane closures.
