State Highway 1 from Dunedin to Palmerston is closed due to flooding this morning as rain continued throughout the night.
The main thoroughfare is also closed further north between Glenavy and St Andrews.
A heavy rain warning remains in place for Dunedin, North Otago and Canterbury south of the Rakaia River.
Dunedin can expect the rain to ease by about 10am and North Otago by about 9am.
Dunedin mayor Aaron Hawkins said the worst of the rain appeared to be over and there were no further evacuations overnight.
"We're expecting a bit more rain over the day ... and we're keeping a watching brief on some of those rivers in outlying townships in particular, but overnight we seem to have dodged a bullet," he said.
There had been no major flooding but Dunedin Civil Defence emergency management were continuing to watch streams and rivers, particulary Lindsay Creek and Water of Leith in North Dunedin.
The Waikouaiti and Taieri Rivers are also being monitored.
Students living in some low-lying North Dunedin flats near the Water of Leith were evacuated last night as flood waters threatened properties.
They were allowed back early this morning and only a small number of people used the evacuation centre at Dunedin North Intermediate overnight.
Campus Watch staff door-knocked about 35 affected properties between Montgomery Ave and Leith St central late yesterday afternoon to warn residents of possible flooding.
A Dunedin City Council spokeswoman said students were told to consider leaving their flats if they had somewhere else to go, and those who chose to remain were asked to have a bag packed and be ready to move at short notice.
Leith St resident Aimie Clark (21), of Christchurch, said she and her flatmates did not leave on the first request, believing they would be safe as long as water did not come through their back fence.
But they got a fright when they were told evacuation was no longer voluntary, she said.
"It’s half and half, a bit scary and an adventure at the same time."She took a bag packed with her passport, a laptop and other electronics, and a change of clothes, and planned to bunk down at a friend’s place.
Blacks Road Grocer was inundated with about 15cm of floodwater in North East Valley yesterday and was too damaged to open today.
As a precaution, several patients were evacuated from the Otago Community Hospice, in North Rd, to Mercy Hospital last night.
The city council had organised an evacuation centre at Dunedin North Intermediate and alternative accommodation options were also available.
In Maheno, flooding concerns forced Maheno School to close early yesterday.
Principal Stella Macrae said she warned parents earlier in the day about the situation and all 64 pupils had been picked up by 2.15pm.
A message would be posted on the school’s Facebook page by 7.30am today to let people know if the school was open.Emergency Management Otago urged people to remain vigilant of water levels in their area overnight, particularly in areas more susceptible to flooding, as the heavy rain continued across Otago.
The slow-moving weather front moved southwards down the South Island yesterday and was expected to continue until late this morning, when the rain was expected to begin easing.
Late last night, Waka Kotahi NZ Transport Agency Otago system manager Graeme Hall said State Highway 1 was likely to close overnight north of Maheno at the Kakanui River and north of Hampden at Big Kuri Creek, because of rising floodwaters.
"There are no detours available, so drivers may need to postpone their journeys," Mr Hall said.
He said the Waikouaiti River and the Shag River/Waihemo were also rising and there was a risk of flooding across SH1 and SH85, respectively.
Those travelling on SH1 north of Dunedin to Waitati were urged to take "extreme care" because of uneven surfaces and surface flooding.
The highway to Port Chalmers (SH88) also had flooding in several places.Near Milton, the intersection of Back Rd and Springfield Rd was also badly affected by flooding.
Many roads around Dunedin itself were closed because of flooding, including Leith Valley Rd between Malvern St and Poulter Rd due to a slip, McGrath Rd (at Waikouaiti River bridge), Surrey St (between Hillside Rd and Ruskin Tce), Ravensburn St (Woodside), Old Brighton Rd (between Walton Park Ave and McMaster Rd), Waitati Valley Rd, Miller Rd (at Waitati River ford), Southdale Rd (at Tautuku Fishing Club), Gladfield Rd (at Silverstream ford), Silverstream Valley Rd (at Silverstream ford) and Flagstaff-Whare Flat Rd, and Portobello Rd (between Marne St and Vauxhall Yacht Club) was closed due to a rockfall hazard.
Otago Regional Council engineering staff were positioned at vulnerable rivers and streams overnight, while emergency services, lifeline agencies and staff from the Clutha District, Waitaki District and Dunedin City Councils watched the situation closely and were prepared to act as events unfolded.
"We’re keeping a very close watching brief on the situation right across Otago, and are ready to escalate if necessary," he said.
In Canterbury, schools closed, businesses were inundated and dozens of roads closed around Christchurch as heavy rain lashed the region.
More than 70mm of rain had fallen in the 24 hours to yesterday afternoon, amid the city’s wettest July on record.
Flooding also forced pupils from Christchurch Girls’ High School to study from home.
Principal Christine O’Neill said it was the first time anyone could remember floodwaters closing the school.
— Additional reporting Rebecca Ryan & RNZ
