RSPCA investigators are likely to lay  charges in the coming days following a raid on  Pets Galore that uncovered multiple alleged breaches of the Animal Care and Protection Act.

But first they must assess and catalogue more than 400 animals seized from the Toowoomba business on Wednesday night.

Toowoomba RSPCA investigator Shaun Jensen said the raid and the number of animals seized was significant and one the largest operations in recent years.

"It is unusual for the region," he said. "We are talking about a large number of rodents and birds.

"Logistically it is a huge job and not just the initial operation at the store but what happens afterwards to ensure the animals' vet needs are met."

The animals are currently housed at the RSPCA Wacol centre.

As the investigation wraps up they will likely be fostered out and adopted.

Mr Jensen said RSPCA animal welfare agents were in talks with Pets Galore owner Nicole Bourne for several months leading to the raid.

"The matter in under investigation and it is highly likely charges will be laid," he said.

"Investigators still need to sift through all the veterinary evidence and there are ongoing investigations at the site."

Pets Galore remains open.

"I am co-operating with the RSPCA as I have always done and I hope their investigation will be resolved soon," Ms Bourne said.

"My team and I look forward to servicing our valued customers as we have for over 30 years now."

The animals seized in the raid included one dog, four cats, one kitten, 65 budgies, 11 quail, four doves, six lovebirds, 19 canaries, three GC conures, 25 Indian ringnecks, 122 finches, 14 guinea pigs, seven rats and about 250 mice.

Raid video, released by RSPCA investigators, showed overcrowded cages, birds missing large sections of feathers and dead fish floating alongside live ones.

Pets Galore has come under fire in the past for alleged mistreatment of animals.

It was the target of a 2017 petition calling for the store to close. It attracted more than 3000 supporters.

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