These included free meals for the elderly and school children, shuttle services to doctors' appointments and care provided for terminally ill and disabled people.
In submissions, the Red Cross, Presbyterian Support Northern, St Vincent De Paul and Waikato Community Hospice Trust urged the council to back down from the proposal to withdraw rates relief given to the charities.
Red Cross' four Hamilton charity shops would go from paying a combined $3141.76 to $25,000 a year - a 795 per cent increase.
St Vincent de Paul was facing a 700 per cent rate jump and Presbyterian Support Northern would incur an 830 per cent increase.
New Zealand Red Cross national retail manager Patrick Cummings said the "increases are exceptionally harsh and will hurt those most in need".
Presbyterian Support Hamilton manager Kim Gouk said the increase could force the body to close its store because it would "seriously jeopardise" its economic viability.
She said the store also provided a role in providing low-cost clothing and items for people on tight budgets.