The burglars appear to have gained entry through a door in the library before ransacking Community House to steal petty cash from a filing cabinet meant for the foodshare program, a donation box for the Leukemia Foundation and other small cash tins.
Staff left Community House on Saturday afternoon and received a call from the cleaners on Sunday to alert them of the break-in.
The thieves appear to have known where the money was hidden and ignored two laptops and an iPad.
"They didn't completely ransack the place so we're fairly confident they knew what they were looking for," a Community House staff member said.
"We provide a safe, comfortable and welcoming environment for all members of our community with no judgement. We provide services far beyond what is expected and work so hard to help our community in any way we can. The staff and volunteers at Community House have been left feeling disappointed and violated that this has happened to us."
Police visited the crime scene today and Community House is asking anyone who may have information to come forward.
Senior Constable Pierce of Rochester Police said the matter has been handed over to the Campaspe Crimes Investigation Unit.
Community House regularly opens its doors for fitness programs, foodshare services, various support groups, art classes and a community kitchen.