A fix to stop millions of litres of sewage continuing to pour into the waters off the coast of New Zealand’s capital, Wellington will be in place by November, officials have said, with full repairs at the cost of NZ$53.5m by late next year.

More than 100 days since the catastrophic failure of the city’s wastewater treatment plant on 4 February, a mix of raw and partially screened human effluent is still being flushed directly into the Pacific Ocean.

In an announcement on Wednesday, Wellington’s mayor, Andrew Little, said the Moa Point wastewater plant would be operational again in six months. Work had begun to assess the damage and clean the plant, with all major repair works to be completed by November. By then, effluent would be removed and the waste products would be mostly treated, with water quality improving to the highest level within weeks.

“People are looking for certainty about when the plant will be up and running, and I’m confident this can be relied upon in terms of a timeline,” Little said, saying it would provide reassurance to hard-hit businesses on Wellington’s South Coast which had faced “massive disruption”. Full restoration of capacity and a fix for the design flaw that caused the failure would be completed by late 2027, officials said.

Wellington residents had mixed feelings about the latest update, saying human and marine health and livelihoods remained at risk. “It would be better if it hadn’t happened, and we should still be significantly worried about the penguins, the dolphins, the fish who are going to be eating raw sewage,” said Nicole Miller, chair of the trust that supports the Taputeranga marine reserve, a network of pristine reefs and underwater ecosystems in the disaster zone.

Destination Kilbirnie general manager Steve Walters said they were disappointed with a longer-than-anticipated timeline. The two dozen businesses most affected – which include diving and water recreation companies – were projected to lose a combined NZ$3-4m in earnings, and that was if the plant was fixed by September. Now, some may not make it through winter. “Our concerns are is this going to happen again,” Walters said. “This is a council failure, and we still have to pay rates, electricity, staff costs. We feel let down, frustrated, and in a state of ‘how are we going to survive this?” A council business subsidy of NZ$200,000 was not enough, and legal action was being considered, he said.

An independent crown review of the disaster is due in August, with two damage reports finding an air bubble in a pipe had likely contributed to the flooding of the treatment plant, destroying 80% of equipment. Since February, sewage has been pouring into the Cook Strait. When it rains, sewage appears just metres offshore, closing beaches.

Wellington Water’s chief operating operator, Charles Barker, told the Guardian they were working “incredibly fast” on the complex plan. “If you look at the scale of the floods, the enormity of the task, it’s not surprising. If this was a house you’d still be in the recovery phase as well.”

The rebuild would focus on preventing another disaster, he said, adding there had been no indication the plant would fail. “Nothing in our understanding of the plant over 30 years led us to believe it couldn’t do what it was designed to do.” The chance of the plant flooding again would be “eliminated” once the work was complete, he said.

The Moa Point facility is owned and overseen by two layers of local government and a council-owned water utility – Wellington Water – which contracts the French-owned waste management company Veolia to run the plant. On 1 July, a new entity called Tiaki Wai – created by the government as part of its water reforms – will take over the Wellington region’s water assets.

The disaster comes as a national Climate Change Commission report highlights the country’s water infrastructure as at major risk of failure during increasing storm events.

Local government and climate change minister Simon Watts said he shared the frustration of local residents. He said “historic underinvestment” in water infrastructure would be addressed by his reforms, including introducing new environmental standards. “Due to the scale of the challenge, and constraints in the sector’s capacity to address it including the financial impact on local government and the public, this will take time.”

Many who initially stayed out of the water had returned despite experiencing sickness. “Surfing’s an addiction, you can’t live without it but you know you’re putting your health at risk,” said local Simon Hurley. Other ocean-goers had reported suffering gastroenteritis, fatigue, chills, and mouth ulcers, or what locals had nicknamed sea ulcers. “It makes you feel uneasy, like ‘Is the water meant to be that colour?’”

Official advice is that the health risk is low unless it has been raining, But effluent can be pushed back into the bay by tides, currents and southerly winds, and human-borne bacteria and viruses are of concern, said Otago University environmental epidemiologist Simon Hales. “The major immediate risk is various infections, and some of these organisms you only need to ingest a tiny amount to get very sick.”

South Coast resident Jamie McCaskill, from the Ngati Tamaterā iwi (tribe), has dived for seafood in the area for more than two decades. His tūpuna (ancestors) had done so for generations. This year, eating it could make them gravely ill. “The way I look at the moana [ocean], the way I feel when I’m out there has changed, and it’s hit the grocery bill, too,” said McCaskill. “We’re all gutted, and it’s like we’ve been forgotten about.”

In the meantime, people like Real Aotearoa business owner Jane Fahy, who is 200 metres away from the beach, are trying not to think about the bacteria alighting on their salt and sand-smudged windows. “I used to call it beach glitter,” she says. “Now I don’t like to think too much about what’s in it.”