The chlorination will take 60 days to start. It will cost $600,000 to do, as well as $20,000 a month in operating costs.
In December, the city lost its secure bore status because assessments found 103 below-ground wellheads were not sufficiently sealed to prevent surface groundwater contamination, especially in heavy rainfall.
City council staff and medical officials found out on December 22. Mayor Lianne Dalziel and elected members were not aware until January 15.
A work programme is under way to upgrade city council wells by December.
In a separate motion, city councillors unanimously voted to accelerate the programme, costing another $840,000.
The water would be chlorinated until the city got back to "secure" status, which is hoped to be done by October.
They also asked for a report, through the infrastructure, transport and environment committee, on any additional costs, and an external review by chief executive Karleen Edwards about the whole situation.
It is currently safe to drink the water – the risk is the chance of future contamination.
Cr Jamie Gough said to keep Christchurch water chlorine free in the future, they needed to do it temporarily now.
In September 2016 the city council went against staff advice and decided not to temporarily chlorinate the water in the northwest of the city, while it upgraded its shallow bores.
Ms Dalziel said she was not prepared to take the risk this time.
"If you look at Havelock North, three to five people died and there were thousands infected. There would be hundreds or thousands potentially exposed here."
Cr Templeton asked if Medical Officer of Health Alistair Humphrey would have preferred the water be chlorinated last month when the risk was discovered.
Dr Humphrey said yes but there had not been a large risk because of the delay.
Cr Templeton also questioned the timeliness of the response, but was shut down by Ms Dalziel.
"There's an assumption there has been a delay in response. This is the first council meeting of the year so there hasn't been a delay in response," Ms Dalziel said.
"Council staff have had delegation on this matter, so they relinquish that this week. I just want to put that to bed."
Cr Yani Johanson and Ms Dalziel asked why the wellheads now did not meet standards when a number of them were upgraded following the February 22, 2011 earthquake.
"I think we do have to look at the quality of the work [inspections] that was undertaken before," Ms Dalziel said.
Additional funding may be required to accelerate the upgrade programme. But it was not yet known how much.
It would be found within the existing maintenance budget. Other things with lesser importance may be deferred.
Dr Humphrey said the city council went above and beyond to keep the water safe.
The city council chlorinated the water following the February 22, 2011 earthquake, he said.
Dr Humphrey could have ordered the city council to chlorinate the water under the Health Act, had the vote gone the other way.
The decision comes after a Government inquiry into the 2016 Havelock North contamination recommended all reticulated drinking water in the country be treated.
The outbreak caused more than 5000 people to become ill with campylobacteriosis, with about 45 hospitalised. It was linked to four deaths.
Dr Humphrey said there was no evidence chlorine at levels put in drinking water caused any health problems.
