Stephen Hunter, deputy secretary and executive director of quarantine, has been replaced by Peter Shergold, who will oversee implementation of a raft of changes recommended in the 343-page report from the Commission of Inquiry into the equine influenza outbreak.
The report by retired judge Ian Callinan was released yesterday with 38 recommendations for change. The federal government has said it will implement all of them.
Callinan's report outlined a litany of failings and shortcomings in the operation of the Australian Quarantine Inspection Services (AQIS) that, in his view, contributed to the escape of the virus from the Eastern Creek Quarantine Centre, near Sydney.
"What I describe bespeaks an organisation that lacked clear lines of communication between those responsible for formulating procedures and work instructions and those responsible for implementing them," he said.
The retired judge said there was insufficient training and education in relation to procedures and instructions to be followed, and no checking to ensure that they were being implemented.
Nor, he said, did AQIS have any business plan or other reporting system to alert senior management to these failures.
There was a lack of effective supervision and monitoring of people entering and leaving the station, which he described as understaffed.
He said the station was not adequately funded to enable it to properly discharge its quarantine management functions, and the national programme was also inadequately funded, he said.
"There was evidence that, had a cogent case been made for additional funding, the government would probably have provided it."
He added that those who treated and cared for the horses in Eastern Creek — especially the grooms, private veterinarians and farriers — and the import agents and studs who employed or retained them, must take some responsibility for the failure of quarantine.
"Their failure to decontaminate themselves and their equipment contributed to the probable means of the virus's escape from Eastern Creek."
Callinan found that one of the four horses from Japan received into Eastern Creek on August 8 - the stallion Snitzel - was likely to have been infected with equine influenza.
It was also possible that one or more of the other horses from Japan that arrived in Sydney with Snitzel might have been contaminated with the virus but not infected by it.
Callinin also found that that some of the horses from Japan received into Spotswood Quarantine Centre on August 8 as part of the same shipment were infected with the virus, but there was no evidence to suggest the virus had escaped from there.
He said: "The most likely explanation for the virus's escape from infected horses at Eastern Creek is that it did so by means of a contaminated person or equipment leaving the Quarantine Station.
"The contaminated person or persons or equipment are most likely to have been those associated with the care of the horses while in quarantine.
"Fundamental biosecurity measures were not being implemented in the largest government-operated animal quarantine station in Australia," he said.
"This constituted a serious failure by those within the Department of Agriculture, Fisheries and Forestry and AQIS, who were and had been responsible for the management of quarantine risks and, in particular, the management of post-entry quarantine arrangements.
"Grooms, private veterinarians and caterers were given access cards and keys that allowed them to enter and leave the Quarantine Station and the equine enclosure at will."
Among the people who ultimately must take responsibility for the failures were the Secretary of the department as the Director of Animal and Plant Quarantine and the person who, under the Minister, is charged with execution of the Quarantine Act 1908, the Executive Director of AQIS and the Executive Manager of Quarantine within AQIS.