It urged the council to put the facility on an open market, whether it decided to continue to lease or sell the building, which has been valued at about $2 million.
YMCA management said the facility was much more than a basketball court.
Executive director Christine Walter said it provided for a much wider sector than just the five sports the new recreation centre was targeting and worked with disabled people as well as running after-school programmes.
YMCA chief executive Peter Fergusson said the not-for-profit organisation's biggest concern was having the building sold from under it.
He said the YMCA could live with reduced or no funding if that was the only option.
It wanted to enter a long-term partnership with the council and would be prepared to spend the required $1 million to $1.5 million on maintenance if it could sign a 20-year lease on the building.
He said the city's $200,000-a-year investment - $90,000 in grants and waived $120,000 to $175,0000 in rent - was returned two-fold to the community as city councillors quizzed him on whether the Hamilton's investment was in line with other councils.
Mr Fergusson said the YMCA would want first option of buying the facility if the council decided to sell, though he was not sure whether it could afford it.
Waikato Kindergarten Association trustee Amanda Beatson said the association also wanted the choice of either buying or leasing the facility to continue key community services.
The association would focus on providing the early childhood programmes and had been talking with Hamilton partners interested in taking over recreational services in the gymnasium, similar to those currently run there.
"The YMCA has enjoyed a privileged position in relation to the Pembroke St site for many years.
"Sell or status quo may not be the only options available."
This week, the Hamilton Community Indoor Recreation Centre urged the city council to use the proceeds from the sale of the building to pay for the first phase of the city's recreation centre.
