Bendigo Animal Shelter president Debbie Edwards said the Regional Partnerships program was intended to be the main source of funding for the $2.5 million facility.

But now the organisation faces funding uncertainty following the Federal Government’s decision to axe the $236 million program.

The Regional Partnerships program has been replaced with another program, but the funding is much less.

Ms Edwards said Bendigo Animal Shelter’s application would be honoured under the new program but the desired amount might not be granted.

"Regional funding is still available but they’ve shaved $200 million off.

"Because the federal side of things is up in the air, we’re revising how we are going to get the funding."

Federal member for Bendigo Steve Gibbons said Regional Partnerships had been axed because it was the subject of an unfavourable assessment by the Commonwealth auditor-general in relation to the previous government’s administration of the program.

"Labor has introduced a new program that will be open to scrutiny, and all submissions will be assessed and prioritised by an independent panel," he said.

BAS needs a combination of local, state and federal funding as well as community donations to build the $2.5 million headquarters in Huntly North.

Located on 30 acres, the environmentally friendly facility will house up to 130 dogs and 100 cats in the shelter and pet boarding facility.

BAS was given the go-ahead to establish the site earlier this year, after the Victorian Civil and Administrative Tribunal overturned an objection.

Ms Edwards said BAS was keen to start building works as soon as possible and urge the community to get behind the project.

BAS has several fundraising initiatives in which the community can donate, including the Buy-a-Brick Program and the Specific Donation Scheme.

For more information on the project, telephone Ms Edwards on 0417 382 741.

Donations can be made at any Bendigo Bank or www.jlbendigoanimalshelter.org.au