The High Court has denied an appeal by Tasmanian councils to overturn a Supreme Court decision that exempts not-for-profit organisations from paying rates.

Retirement Village operator Southern Cross successfully took a case against the council last year as they faced a $564,000 increase to their rates.

Hobart Lord Mayor Anna Reynolds said the decision will force a council rethink as more organisations claim the charitable rates exemption, and that they will have to work out how to make up the funds.