A new bypass pipe installed in Parnell has reduced the sewage discharged into the Waitematā Harbour but has not stopped it, Watercare says.

It has been three weeks since a waste and stormwater pipe burst under a 13-metre-deep sinkhole in a central Parnell car park.

Crews have since created a 400-metre long above-ground bypass pipe to skip the broken section and stop hundreds of litres of wastewater flowing into the ocean every second.

Watercare head of service delivery Sharon Danks told Morning Report water samples were being taken from the ocean to measure the environmental impacts of the sewage overflow.

"The pumps are running from today, it'll be a slow ramp up over the next couple of days because there's a few things that we need to do ahead of the pumps being at full capacity."

This included pumping down all of the water that was stored in the main and resolving the overflows fully.

"The sewage is still overflowing into the Waitematā right now and it will be over the next day or two but it will be with decreasing volumes as the pumps pump down."

Overflows would still occur in wet weather, she said.

"And they probably will occur more often than they occur in normal circumstances. 'Cause of the catchments being combined catchments which take a lot of stormwater as well there is always a risk of wet weather overflow in this catchment."

Sinkhole in Parnell Photo: Watercare

Banks said it was a huge milestone for Watercare that the pumps were running.

She said the underground pipe was still blocked and it was hoped this would be unblocked in the coming few weeks.

Rehabilitating and repairing a larger section of the main was likely to take about five months, she said.

Some beaches still unsafe to fish and swim in

Auckland Council's Healthy Waters is continuing to monitor water quality over 40 beaches, and about 20 are still marked as unsafe to swim in by Safeswim.

Watercare chief operations officer Mark Bourne said environmental monitoring of the harbour was also ongoing, including the sampling of oysters for pollutants like heavy metals and viruses.

The gathering of kaimoana across those affected beaches was still strictly off limits, Bourne said.

Deputy mayor Desley Simpson said even after Safeswim marked a beach as safe, people were advised not to eat seafood from those areas until 28 days later.

Meanwhile, beachgoer Te Ngakau Rakete said officials had taken too long to stop the overflow.

"It's a long time when you think about three weeks of sewage flowing into the ocean, that's horrendous actually, when I think about it, I'm very shocked to hear that it's taken that long."

Te Ngakau Rakete, who was visiting Okahu Bay on Tuesday, said it was disappointing there was no water quality warning signage in the area.

Orakei local Carmen Goodwin said the Parnell sinkhole incident reflected a wider problem.

"I think it's probably a systemic problem in making sure that infrastructure is up kept, and I don't think it's a surprise but it's a shock that it's come at such an extent."

Goodwin would like to see more communication from officials.

"A little bit of transparency perhaps around what the issues are, it seems to be everything comes to a crisis and action is taken that is very last minute approach."

Auckland Council alcohol and environmental health manager Mervyn Chetty said there were water quality warning signs at all locations marked as unsafe by Safeswim, including "no fishing" signs at Okahu Bay Wharf.

Chetty said they had sent an officer to check if the signage was still in place at Okahu Bay.