Metservice meteorologist Tom Adams said damaging winds in Wellington city might begin about 8pm, and would reach their peak at 4-5am.
The 140km/h gusts were only expected for exposed, high areas. Wellington city might get gusts up to 100km/h, he said.
Heavy rain was also expected but Wellington was not under a weather warning for rain, Adams said.
A spokesperson for the Wellington Regional Emergency Management Office said "hundreds" of people were evacuated from homes and apartments after the quake, though few hotels had been evacuated.
However only one person needed assistance to find somewhere to stay, while the others had all gone to stay with friends or family.
Lester told gathered media the city was "in really good shape" considering the size of the earthquake but warned people to stay out of the CBD, which was already uncharacteristically quiet, if not completely deserted.
"For the most part, infrastructure's holding up really well, but we do have assessors going out there at the moment assessing each building," he said.
Most of the damage was "superficial" but people would be kept out of affected buildings until engineers and assessors were sure they were safe.
"We don't want people going into buildings if there's a risk of something falling on them," Lester said.
Fourteen Urban Search and Rescue members have travelled to Wellington from Palmerston North to assess buildings. They will be using drone technology to help.
Kiwi Property says its buildings in Wellington have been cleared verbally by structural engineers, but the official sign off is yet to be given.
These buildings included the Majestic Centre, the Aurora Centre, and 44 The Terrace, as well as Porirua's North City Shopping Centre.
Formal engineering reports and final building checks are still needed before the buildings can be occupied again.
In the South Island, where the earthquake struck, numerous helicopter companies have their entire fleet out moving people around the country and surveying damage.
Christchurch Helicopter pilot Kevin Walsh said all four of their choppers are helping out and they might be overnighting at Cheviot.
"The phones are ringing red hot I'm just trying to do all the logistics.
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• Our live updates as the latest unfolds around the country after today's earthqaukes
"Basically they just haven't stopped."
Walsh said the pilots are moving Civil Defense personnel around, checking roads and surveying damaged infrastructure. He explained one of the biggest challenges is communication as there is limited cellular service and the power is still down in certain areas.
Reid Helicopters Nelson officer manager Caroline Church said the weather is starting to turn for the worst.
"I'm just making sure they're safe as the weather is pretty horrible too... The gods are angry.
"It is what it is and we're doing what we can to help."
Garden City Helicopters' 10-strong fleet are all out in relation to the quake.
