"It wasn't a lot of money they took - but it's pretty sick," Mr Sewell said.
"My guess is someone was at our event, saw us shaking the buckets, and thought, 'oh, there'll be some money in there tonight'.
"I suppose they felt they were more entitled to it than our animals."
Mr Sewell said the donated money was kept "under lock and key" in one of the cabinets - and suspects the thief or thieves searched the building for the key.
Police have said the window was forced open, with the culprit likely using an object to prise the seal from the window frame, leaving them able to reach in and open the latch.
"The rubber seal has been damaged - I think they may have used a piece of metal.
"The police say these were people who knew what they were doing."
Mr Sewell said this is not the first time in 2015 the centre has been targeted.
Earlier in the year, a person attempted to break in and triggered the burglar alarm, while another raided one of the storage units, making off with three bags of animal feed.
He said the thefts were "disappointing" for the centre, already cash-strapped after an investigation into the employment of former manager Lloyd Warren.
Donations and bequests dropped dramatically throughout 2014.
"Our finances took a hit.
"We're not a rich centre anyway - we're not Wellington or Auckland which has the large numbers of donations, so it's been difficult."
This year, with new front desk staff and a new committee, Mr Sewell said the centre's fortunes were changing, with fundraising efforts bringing in $8000 as of January.
He encouraged anyone who had seen anything suspicious, either at the Children's Day event or on Sunday night, to contact the police.
The centre is also accepting donations to replace the stolen money.
"If you did steal the money, do the right thing and hand it in.
"It's for our animals - that's the only reason any of us are here."
