The 8 million litres of water in the basement of the SkyCity convention centre has been deemed safe enough to be pumped into the wastewater system rather than straight out to sea.
There were fears the water would be too toxic to be treated and would end up in the Waitematā Harbour and become an environmental hazard.
There are still around 100 cars in the convention centre's lower carpark, semi-submerged - and some floating - in about a metre and a half of the water.
Firefighters have set up oil booms to try and separate the worst of the contaminants from the water and, until the test results came in last night, it was being pumped into the stormwater system and out to sea.
Nick Vigar, from Auckland Council's SafeSwim programme, said it was a big relief to instead send the water into wastewater manholes.
"It was an unknown quantity, to be sure. I guess it gives us some reassurance that the water we did pump into the harbour is not particularly contaminated, but we'll continue to test," he said.
"We're still waiting for the results of our water tests from [yesterday] and some of those eco-toxicology tests, which [look at] the impact on organisms. We won't know that for something like three days."
Mr Vigar said the water was currently being pumped out at about 25 litres a second, and it would take about four days to drain the basement, but it could be longer depending on how much more water was needed to damp down hot spots.
"The flow rate's being looked at very carefully in terms of not creating overflows on the wasterwater network, 'cause obviously that would be a problem.
"We have crews out who are checking the wastewater network to ensure that's not creating a problem."
Beaches near the Auckland waterfront remain closed, with a hazard alert in place at St Mary's Bay, and will remain so until sea water is tested and found to be clear of any contamination.
But Mr Vigar was confident there was not going to be any long-term problems as summer approaches.
"On the back of some results that are indicating that the contamination was possibly not as bad as we feared, for those beaches further away from the source I think the dilution is sufficient that we probably don't have any significant issue. That's significant for Labour Weekend as well."
Water quality scientist Tara Okan explained why it wouldn't have been possible for the water to be treated at the wastewater facility if it had been deemed too toxic.
"A water treatment plant is a giant farm - you've got billions of little animals in there and they need food and they need oxygen.
"And they need clean food because if you gave them poisonous food the bugs die. And if the bugs die then we don't get wastewater treatment and we start putting ammonia into our sea, and it's toxic and it kills the sea life."
He said it was great news that the water would not end up in the Waitematā, and he was confident that Watercare wouldn't have allowed water into one of its treatment facilities if it risked killing the micro organisms so vital to cleaning the city's waste.
"Their job is to protect their own plant and if they've carried out tests and decided that the plant is not negatively affected then that's a good solution.
"You're talking 8 million litres. Well, a million people are going to produce more than 300,000 cubic metres - so that's 300 million litres - per day. So 8 million isn't that much when you put it into 300 million litres."
SkyCity has promised to compensate the owners of the cars that were damaged.