Waikato Regional Council says the impact of heavy rain is likely to be felt over the next three days with rising river levels, as flood waters come down from hill catchments.
The areas of concern are Coromandel, the Hauraki Plains and Taupo.
The council says Lake Taupo is approaching its maximum control level (357.25m above sea level), with work continuing to lower it by spilling more water into the Waikato River.
The Waikato River in the hill country east of Te Kuiti and Otorohanga received about 200 millimetres of rain in 24 hours and is expected to peak on Tuesday at Ngaruawahia, where it converges with the Waipa River.
The council says it's working closely with Mighty River Power to manage flows through the Waikato River hydro system.
Floodwaters blocked some Waikato roads and closed the Spa Thermal Park camp ground in Taupo on Sunday.
Flooding also closed State Highway One between Waiouru and Turangi.
Civil Defence says people living close to rivers and lakes should prepare for rising water levels over the next three days as heavy rain continues to fall, particularly across the Coromandel Peninsula, Hauraki Plains and Taupo area.
Bay of Plenty
Civil Defence in Whakatane says predicted levels of heavy rainfall didn't eventuate on Sunday but it's still concerned about forecasts of heavy rain overnight and on Monday morning.
Three roads in Whakatane and Ohope were affected by surface flooding and four streets in Edgecumbe were closed.
Whakatane Civil Defence Controller, Diane Turner, says while there has been some localised flooding, the rain that fell on Sunday wasn't as serious as originally forecast.
She says the main concern is the rain that is forecast in the hills and what impact that may have on rivers over the next 24 hours.
The Matata Motor camp in Bay of Plenty was closed because of flooding on an access road.
On the east coast of Northland, where 200mm of rain fell overnight on Saturday, part of Rawhiti Road near Taupiri Bay collapsed.
Police advised people to restrict travel on the Coromandel Peninsula around Whitianga due to floods, slips and fallen trees, after nearly 100mm of rain was recorded in a 24-hour period since Saturday.
Police urged motorists driving over the Kaimai Ranges to take care due to surface flooding.
The Desert Road, SH1, was still closed because of flooding on Sunday night.
Rivers at high levels
Farmers in parts of Northland, Bay of Plenty and Waikato have been told to move stock to higher ground.
Bay of Plenty Regional Council said several rivers in the region had reached early warning levels after 100mm of rain fell in eastern Bay of Plenty in 24 hours.
The Otara, Waimana, Waioeka and Mangorewa rivers reached their first warning levels on Sunday morning and council staff were preparing pumping stations.
Bad weather also forced the cancellation of the final day of the popular Wings Over Wairarapa air show at Masterton.