Many were baffled as to why their properties were identified as having a flood-risk when they were elevated, had already mitigated flooding concerns or had received a letter when a neighbour hadn't.
Ms Hardaker said the process was "unnecessary" and "handled badly".
"The communication over the past few days has been unacceptable, leaving people unnecessarily confused and uncertain."
Ms Hardaker rejected claims her hands-off approach to operational issues as part of her governance-focused approach was to blame, but said staff needed to realise potential impacts on ratepayers. She has ordered an immediate review of the process.
Staff have been told nothing was to be added to Lim reports until the properties were reassessed, property owners had a chance to respond and elected members signed off exactly what went in the report.
Councillor Ewan Wilson called the letters "alarmist" and councillor Dave Macpherson said the council should have given property owners all the information upfront rather than scaring them. He has called for the elected wing to get more involved in the day-to-day running of the council.
"[This] hasn't been handled well ... if we had a system of checks and balances before [the letters] went out to members of the public we wouldn't have had this."
Problems with the district plan consultation process were compounded on Sunday when councillors were advised a second "vague" letter had been sent to 450 homeowners telling them they could be blocked from making any changes because they were close to high-voltage transmission lines.
But Ms Hardaker said the council was required by legislation to protect the power-line corridor and staff had urgently updated its website with clearer information.
The draft district plan feedback process will continue but Ms Hardaker said she had given management clear expectations of how it was to be handled.
Waikato Property Investors Association president Nancy Caiger was relieved the council had responded to the public outcry, but said it shouldn't have got to that stage.
Mrs Caiger, who got three flood-risk letters relating to her properties and one high-voltage letter, said it was important owners had the chance to respond because ultimately any information put on a Lim report would make people think twice about a purchase.
Waikato Property Council vice-president Graham Dwyer said it appeared to be a reflection of systemic problems with the Hamilton City Council and its employees.
The open days for flood-risk and properties near high-voltage transmission lines will continue. Yesterday afternoon property owners packed into the Western Community Centre in Nawton to find out more about their properties having a flood risk.