Paul Van Buynder, Chief Medical Health Officer for Fraser Health, said the move was "necessary to ensure a safe drinking water supply."
"Over the years, the water system had been compromised on many occasions resulting in fecal coliform and E. coli bacteria," Van Buynder said in a statement.
"I recognize that the outcome is not what many of Chilliwack residents had hoped for, but given the system vulnerabilities, no other option meets required drinking water safety standards."
The city’s emergency chlorination system must now be upgraded to a permanent, full time system. The change will cost the city an estimated $1.5 million and residents in Chilliwack can expect an increase of three percent increase in water user fees.
Mayor Sharon Gaetz said she was extremely disappointed with the news.
"Everyone in the city is disappointed. I cannot think of an issue that's been more strongly fought in the community,” Gaetz said on Thursday.
Chilliwack resident Kim Reimer, who has organized an online petition against the chlorination, told CBC News the battle isn't over.
"We're not done, we're going to continue to fight for the fact that nobody had a say,” Reimer said.
In early February, Fraser Health ordered the city to chlorinate their water after previous tests showed traces of E.Coli bacteria.
Weeks later, Chilliwack started emergency chlorination of its water system after E. coli was found in the Greendale area of the city.
Van Buynder said a subsequent investigation carried out by city staff confirmed vulnerabilities in the system including "a number of residences with dual systems and without backflow prevention ... by which pathogens can enter the distribution system."