ABC News reports that the $300 million centre will be built at Mickleham replacing five outdated quarantine centres across four states.

Large poultry companies say the project could compromise Australia's biosecurity leading to disease outbreaks and even encouraging smuggling.

Daniel Gowland and his family are based at Bungendore, near Canberra, and have been importing and breeding birds for more than 30 years.

Mr Gowland says exotic diseases such as bird flu are a constant threat.

He is one of many in the industry who are concerned about biosecurity measures at the new centre.

"A lot of these avian diseases will come across to humans," he said.

"If we get nailed, the Australian ecosystem that is by far the greatest tragedy in this whole little drama."

The quarantine centre was approved by a federal parliamentary committee and will replace five outdated facilities at Eastern Creek in New South Wales, Knoxfield and Spotswood in Victoria, Torrens Island in South Australia and Byford in Western Australia.

The centre will house all kinds of animals including dogs, cats, alpacas, thoroughbred horses and even bees.

But the birds have been the biggest problem.

A coalition of five major importers that supply the poultry industry told the parliamentary committee the design of the centre is flawed.

The companies said the importation of birds and eggs at the same site could lead to cross contamination and disease outbreak.

"The consequences of failure at this level could cripple the business and even the industry," the importers said.

An independent panel of experts was called in to advise the parliamentary committee and found the design of the facility "has the necessary features to ensure bio-containment of an exotic disease outbreak."

Expert avian vet Peter Scott was on that panel.

"Clearly the Torrens Island group has been a little bit unhappy and they have been concerned about some potential biosecurity aspects there.

"But these concerns have been explained to them and I'm very confident that the measures the Government have in place will allay those concerns."

He says the quarantine chambers will use air filtering, waste management and strict staff protocols to contain any disease outbreak.

The Federal Department of Agriculture says the co-location of birds and eggs is common overseas, and has been used successfully at CSIRO facilities in Australia for more than 25 years.

It also says the new centre provides industry with three times the capacity currently available.