A state of emergency is in place in Ngongotaha near Rotorua after a stream burst forcing the evacuation of about 30 homes.
Properties on Western Road and in surrounding streets were evacuated late this afternoon after the Ngongotaha Stream burst its banks.
Some of those who evacuated said there was no warning and they only had a few minutes to get out.
Some homes were flooded and others had water reaching the top step as residents were leaving.
Rotorua Mayor Steve Chadwick said more heavy rains were expected tonight and emergency services wanted locals out of their houses as a precaution.
Earlier in the day heavy rain caused flooding in various parts of the city and a Civil Defence welfare centre was set up in Rotorua for people who had been evacuated.
Representatives from Civil Defence, the Red Cross and government departments such as Housing New Zealand were at the centre earlier in the day.
Twelve customers and 20 staff were safely evacuated from the tourist attraction Agrodome in Rotorua. Earlier Fire and Emergency said 200 people were stuck there.
An Agrodome spokeswoman said customers and staff were evacuated to a clear road, where they were collected by taxis and buses. Agrodome will stay closed tomorrow.
Tonight, all people evacuated from their homes are either with friends or family tonight or in accommodation arranged by Civil Defence.
In Rotorua, roads turned into rivers, submerging vehicles after more than 100-millimetres of rain fell in 24 hours.
NIWA tweeted that Rotorua had its wettest hour on record with 51.8mm of rain falling between 10-11am, with a total of 167.8mm of rain falling between 4am on Saturday and 6pm on Sunday.
Rotorua had its wettest hour on record (any day, any month) today with 51.8 mm between 10-11 am!— NIWA Weather (@NiwaWeather) April 29, 2018
Hourly records began 54 years ago in 1964.
In total, the town recorded 167.8 mm between 4am Sat-6pm Sun, or nearly 1.5 times the April monthly normal in 38 hours. pic.twitter.com/mwpCqDWJEQ
Rotorua Lakes Council's Emergency Operations Centre has been activated and Civil Defence teams have been mobilised.
The rainfall has also overwhelmed the sewerage system, and the council said all surface water should be treated as contaminated. It's caused overflowing and diluted sewage to overflow the system, entering the stream and lake.
The city's Civil Defence controller Bruce Horne said heavy surface flooding was affecting roads and the sewerage system.
"We haven't got any roads closed yet but we have had some roads that have been affected by the volume of water so we're getting those checked out by contractors at the moment.
"Our stormwater and sewerage has been placed under a lot of pressure. At the moment we're coping, but just.
"There's one or two people that have seen it this bad before but most of us haven't," Mr Horne said.
Mr Horne said the rain had started to ease, but it was not over yet.
"There was a lot of surface flooding which rose up very quickly, a lot of that has now subsided which we're very grateful for, but we're mindful we've still got a bit of bad weather to come, we're not out of the woods yet."
Fire and Emergency crews have had more than 100 call outs to flooding-related jobs throughout the day.
Northern shift manager Scott Osmond said off-duty crews had been brought in, and about 30 fire officers were working to help people whose homes had flooded.
"We started at about 8.30 this morning in the Rotorua area and since then we've had about 140 call-outs to various emergencies but almost all is in relation to the rainfall," he said.
"Unfortunately there's been a lot of cases where we haven't been able to do much because the water level's up outside anyhow so there's no point pumping water into more water."
Mr Osmond said crews would remain on standby.
"There is another rain band heading towards that area so the weather warnings are in force until late tonight or early in the morning."
There had been widespread surface flooding throughout the city, the council said.
Trees are down, there are slips on several roads and water is flooding properties and entering some homes and garages.
Stormwater covers have popped up in some places and residents have been urged to drive only if absolutely necessary.
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Crews from Infracore, Fulton Hogan, Higgins and Fire and Emergency New Zealand have attended more than 60 flooding issues and are prioritising where there is a danger to people and their properties.
Coromandel residents are being asked to take care as heavy rain hits the east of the peninsula.
MetService was expecting another 60 to 90 millimetres to fall, on top of the rain the area's already had.
More than 165mm of rain has fallen in the past 24 hours with surface flooding closing some roads between the Peninsula and Waihi.
MetService has forecast 25 to 40mm of rain per hour in Coromandel this afternoon.
Flooding has closed the road between Whiritoa Beach Road and Whangamatā.
Coromandel Thames District mayor Sandra Goudie said there was likely to be a lot of weekend traffic in the area, and people should drive cautiously and be aware of the conditions.
The Transport Agency is advising motorists to take extra care when driving between Whangamatā to Whiritoa along State Highway 25, where there is surface flooding.
Thames-Coromandel Civil Defence controller Garry Towler said more roads could be closed and with high tide around 6.20pm this evening, more surface flooding was likely.
MetService said there was a risk of severe thunderstorms in Coromandel Peninsula and Bay of Plenty this afternoon, bringing with it surface and or flash flooding, slips, and hazardous driving conditions.
RNZ journalist Carol Stiles was driving in the area and said roads had surface flooding and were treacherous to drive on.
Three homes have been evacuated in Timaru after a bank collapsed on one of them in heavy rain.
The council asked those living in the homes to leave for the evening as a precaution, as more rain is forecast.
Parts of Canterbury were also bearing the brunt of the wet weather with surface flooding along parts of State Highway 1 between Timaru and the Waimate Junction.
Heavy rain is expected in Rakaia, the Richmond ranges, and parts of Marlborough.
Meanwhile, rivers across Otago are being watched this afternoon.
There is a heavy rain warning for Dunedin, north Otago and north of Otago Peninsula until 8pm tonight.
A further 40mm of rain may still be to come.
The Pomahaka River was at its peak in some parts, the Otago Regional Council said. All other rivers in the area were holding well and no major flooding was expected, it said.