Manley says those areas are likely to be flooded again during high tide at midnight.
He has sent workers to shore up the Herald Is properties with sandbags.
"Those properties will remain evacuated overnight. People will keep away from those areas."
The weather has cut power in Remuera and in Mt Wellington, while in west Auckland, residents at Piha, Titirangi and Henderson have been without electricity.
Vector says it has been working on fixing the fault, but some areas may be without power because of damage to service lines.
And Weatherwatch.co.nz head analyst Philip Duncan says the flooding will be intensified by the centre of a large low passing over Auckland at the same time as it experiences high tide.
That centre is about the size of Tasmania and could cause a storm surge which will raise sea levels, he says.
"It acts as a large scale vacuum cleaner and it pulls up the sea with it."
"Coupled with the storm surge we also have the strong to gale force winds which will tonight strengthen further ahead of the centre - driving more water up.
"With that comes more flooding."
Drivers are being warned to take extra care with many slips across the North Island and a lot of surface water.
Motorists were advised to take extra caution on State Highway 2 between Napier and Wairoa, SH 3 from Wanganui to Taranaki, SH4 from Wanganui to Raetihi and SH5 from Napier to Taupo due to minor slips and surface water on roads.
There were also reports of flooding and a vehicle crash due to wet roads on State Highway 1 north of Waiouru, and the Desert Road between Waiouru and Turangi had closed.
A car collided with a fallen tree in the Waikato just after 6am, in what was not a serious crash but closed Maungatautari Road.
Further south, weather had forced the cancellation of the flying programme at Wings Over Wairarapa.
Meanwhile, fears for low lying Central North Island communities are rising as the region continues to be battered by intense rainfall and strong winds.
An Environment Waikato spokeswoman says about 300 campers were evacuated from the low-lying Spa Park near Taupo this morning amid fears about rising river and lake levels.
Forecasters are predicting up to 200mm of rain for the area in the next two days, which could cause widespread flooding, she says.
Waikato Civil Defence duty officer Adam Munro says many Waikato water catchments are already reaching saturation levels.
While Coromandel Peninsula, Hauraki Plains and Lake Taupo are of particular concern, high river levels are also expected in the slower moving Waipa and Waikato Rivers, with forecast flows approaching those seen during devastating floods in 2004, he says.
"In that event, low-lying rural areas around Otorohanga, Huntly and Gordonton were flooded for several days," he said.
"The severity of the flood will depend on the amount of rain that falls over the next 48 hours so Environment Waikato will be keeping a close watch on river and rainfall levels."
The Fire Service responded to more than 100 weather-related events this morning in the northern region, but heavy rain had eased in Auckland and Northland by early afternoon.
Worst affected areas were Auckland's North Shore, eastern suburbs and the lower CBD, said fire service northern shift manager Jaron Phillips.
Major arterial roads in Auckland remain closed by the flooding from the deluge that hit the city this morning.
The northwestern motorway has reopened after floodwater from a king tide closed the citybound lanes at Patiki Road, while surface water is still cutting off motorists at Tamaki Dr and Quay St.
A southbound section of the Northern Motorway (SH1) near the Harbour Bridge was also closed by tidal flooding for about an hour this afternoon. The storm also affected communication links to some electronic message boards on the motorway network, and there were slips on the Brynderwyns on SH1 and flooding near Paihia on SH11 in Northland.
Flooding fears have eased in Northland after forecasters downgraded a severe weather warning, just three hours after predicting a day of massive rainfall in the region.
Metservice issued the warning that 100-150mm of rain would fall by 10pm in Northland at 9am today.
It revised that prediction to 20-40mm before 12pm
Northland Regional Council Civil Defence manager Graeme MacDonald says the occasional rainfall and few heavy falls could cause surface flooding.
But he expects far less damage to the region than originally predicted.
Northland received almost 240mm of rain in the 30 hours to 6am today - more than double the region's average monthly rainfall of about 105mm.
River and rainfall data from throughout Northland is automatically posted at two hour intervals on the Regional Council's website.
The MetService has said the heavy rain was expected to be significant for most regions from Northland down to Waitomo and the central North Island high country, and across the Bay of Plenty to Gisborne and Hawkes Bay.
The heaviest rain was expected to be in Northland, Coromandel Peninsula, Bay of Plenty, the central high country and the ranges of Gisborne and Hawke's Bay.
Bronwyn Campbell of the Bay of Plenty Regional Council said rivers were rising steadily.
"With the current forecast, it is expected the our rivers will peak from early tomorrow morning through to early afternoon tomorrow," Ms Campbell said.
The situation was under control and any minor problems were being dealt with quickly, she said.
"We understand that there is some localised and surface flooding throughout the region, however this is been attended to by local Council staff."
- with NZPA and NEWSTALK ZB
