Australia's chief veterinary officer, Dr Andy Carroll, said all horses at the centre of the scare have returned negative results for equine influenza and have also tested negative for equine viral arteritis.
"Some horses tested positive for equine herpes virus 4, which is already present in Australia and causes mild symptoms similar to the common cold," he said.
"However, all illness appears to have resolved."
Dr Carroll said the Australian Quarantine and Inspection Service has started cleaning and disinfection work ahead of the next arrival of stallions at the facility, near Sydney.
Authorities announced a week ago there was an outbreak of a respiratory disease among horses at the station, but stressed there was no cause for concern.
Equine herpes virus 4 was considered the most likely cause, although one horse had returned what they called a "mild serological reaction" to equine influenza (EI).
"This is not unusual because all the horses have been vaccinated against EI," Dr Carroll said at the time.
"All horses will all be tested repeatedly to make absolutely sure there is no EI circulating before they are released from quarantine," he added.
Dr Carroll said the incident reinforced the need for three weeks of post-arrival quarantine when consignments from different origins are commingled for the first time.