"Hendra Virus is very rare and the circumstances surrounding this outbreak even rarer," Queenland Primary Industries Minister Tim Mulherin said in announcing the aid.
The Redlands practice will get the help through the Australian Veterinary Association's Animal Welfare Trust.
The decision resulted from a meeting between Mulherin and clinic owner David Lovell.
The one-off payment will be given to the Australian Veterinary Association (AVA) which will work with the practice to respond to biosecurity and animal welfare management costs imposed on the business due to the long quarantine period.
Mulherin said extraordinary circumstances associated with the outbreak, including the long quarantine time, the risk to human health and the welfare of the animals quarantined, led to the special assistance.
"Government does not compensate business for loss of trade due to a disease outbreak or similar emergency situation. For example, businesses in the horse industry were not compensated for loss of trade during the equine influenza outbreak. Matters relating to business continuity are a commercial decision for the individual business.
"What we are doing is beyond what legislation outlines during a disease outbreak but this is an extraordinary case and the AVA and the government are responding to it as such," he said.
Biosecurity Queensland and Queensland Health have been working with the clinic since the outbreak first occurred in early July. The support includes:
To date, this research has made good progress on understanding the genetic makeup of the virus, how it affects the body and its behaviour in fruit bat populations, which is the natural reservoir of the virus.
Further research is being conducted into how it is transmitted and the characteristics of the different strains, the minister said.
Hendra is named after the Brisbane suburb where the dangerous virus was first isolated during an outbreak in 1994 which killed horse trainer Vic Rail.
Two staff of the clinic - a vet and senior nurse - remain in hospital after becoming infected by the virus.
The clinic could reopen in a fortnight provided there are no setbacks.
Meanwhile, ABC News has reported the quarantining of a stable near Ballina racecourse pending results on a horse that displayed Hendra-like symptoms.