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The streets surrounding the SkyCity Convention Centre could remain closed for "up to a week", with fire crews still in "active firefighting mode" at the site.
Fire and Emergency say they want to reduce the disruption to CBD traffic, but say they will be moving a large crane into Nelson St tomorrow.
Fire crews tackling the blaze are still in "active firefighting mode" and are being confronted with pockets of flames today.
Fire and Emergency incident controller Dave Woon said today's work also included an "overhaul" phase as firefighters pull off iron and roofing and sealing materials from the roof.
While firefighters hope to reduce their "footprint" around the scene a large crane will be set up in Nelson St tomorrow.
Woon told reporters that fire crews had done an "outstanding job".
"We still have active fire fighting going on. There are still fires in pockets," he said.
Mike Shaw, who is leading the recovery team said: "This is new to us from an urban perspective, this is the first time we've put a recovery team together.
"We're working with all the local stakeholders and business to make sure that everything gets back to normal."
Shaw said it is was hard to say how long the surrounding CBD roads would remain closed.
"It may take a couple of days, or up to a week."
Shaw said they were in communication with Worksafe, Civil Defence and Fire and Emergency.
Six days to pump out flooded basement
Safeswim programme manager Nick Vigar said it would take up to six days to pump water out from the flooded basement carpark.
Water was originally pumped into the stormwater network for 20 hours, but was switched to the wastewater network from 6.30pm yesterday when their testing confirmed that run-off contamination levels were "sufficiently low".
"Our main concern was that emergency services needed to pump water from an immediately dangerous situation."
Vigar said the water in the basement had some hydro-carbon contamination and could be sufficiently treated at a wastewater treatment plant.
They are still waiting for eco-toxicology results which are expected to come in after the weekend.
Vigar advises the public to treat water as potentially hazardous, and there were some reports the water was 'not particularly discoloured'.
He said he doesn't expect contamination levels to increase while cars are in the flooded basement.
Still got a whole lot of work to be done: Mayor Goff
Meanwhile Auckland mayor Phil Goff is feeling positive after a hectic week of 4.30am starts since one of Auckland's biggest fires in recent years broke downtown on Tuesday.
"I'm breathing in fresh air and I won't need to get my suit dry-cleaned at the end of today - which is good, because I was running out of suits,'' he laughed.
The mayor said he had been briefed at 5am and then constantly throughout this morning by authorities about the situation.
All indications is that the fire at SkyCity's new convention centre is definitely out - save for a few hot spots needing to be put out every so often.
"We're really on top of that now. We've still got a whole lot of work to be done, but it's getting back to business as usual in the city centre''.
There have been more flame flare-ups atop the SkyCity Convention Centre overnight.
Fire and Emergency confirmed crews were attacking two incidents this morning.
"These are expected from time to time," FENZ said.
SkyCity CEO Graeme Stephens said it would be weeks before the convention centre was secure enough to properly assess the damage, and at least a month or two before they knew exactly how much damage there was.
Fenz said firefighters were moving to a "recovery phase", which involved finding and extinguishing hotspots in the roof structure as well as any fire inside over the next few days.
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That also involved clearing out about eight million litres of water, contaminated by burning materials, that had accumulated in the Convention Centre's basement carpark.
Watercare estimated the firefight had used nearly 30 million litres of water.
Auckland Council's Safeswim manager Nick Vigar said that water had initially been pumped into the stormwater network and out to the Viaduct basin around Beaumont St.
A swimming alert was issued for nearby St Mary's Bay.
By last night it had been transferred to the wastewater network, after Watercare confirmed the Māngere Wastewater Treatment Plant could handle the contaminated water.
A council spokeswoman said they were not sure exactly how much contaminated water had entered the Hauraki Gulf, and water testing was still being completed.
Hauraki Gulf Forum deputy chair Moana Tamaariki-Pohe said the damage to the harbour's sensitive ecosystems could potentially be "devastating".
"It will have huge impacts. Our stormwater system needs to be prepared to handle this so it doesn't happen again. The Gulf is already stressed, and adding all of this contamination is hugely devastating."
The accumulated water had also flooded about 100 parked cars, all belonging to SkyCity staff members.
Stephens said staff would be compensated for any damage to their vehicles.
While emergency services had now entered the fire-damaged convention centre, he had not yet received any direct reports on the extent.
Yesterday they had been focusing on preparing the existing SkyCity sites to reopen, with the casino opening last night, Sky Tower expected to open this morning and hotel this afternoon.