Mr Dalton said they were taking an ultra-conservative view.
"People need to realise because of Havelock North there is a heightened awareness of potential problems with waterborne issues."
Council were now testing more often and had changed from standard testing to enumerated.
This meant a reading for E coli was given between 0 and 10, with 10 being the minimum at which a boil notice was activated.
"Previously staff would only tell us if the count got above 10 but now we action when it is one. The next count is 0 so it is the lowest level determinable," Mr Dalton said.
Napier City Council's manager asset strategy, Chris Dolley said after having such a high number of transgressions, which came as a surprise, council were rolling out a series of planned improvements to the entire water network along with this period of chlorination.
Mr Dolley said these improvements would concentrate on modifying or completely overhauling the testing points - the places where water was drawn for regular testing - because these sites could be sources of contamination, which result in positive tests.
In the meantime, a secure chlorine dosing site had been established in Taradale, injecting chlorine into the reticulated system 24 hours a day, for as long as is needed.
All of Napier, with the exception of Otatara and Puketapu, is being chlorinated. This means that the smell or taste of chlorine may be detectable in the water in Taradale, Bayview and the central suburbs of Napier.
Daily testing will continue and schools, businesses and tourism operators were being notified of the chlorination today.
A chlorine-free tap, drawing water from the unaffected Otatara and Puketapu area, will be established as soon as possible.
Napier residents can expect regular water updates via Facebook, radio and newspapers, and other channels as the chlorination programme continues.