The Japan Racing Association cancelled horse races last weekend for the first time in 35 years at the Kokura, Niigata and Sapporo racecourses in order to prevent fresh outbreaks.
The association said last Friday that 29 out of the 163 horses who were to take part in the weekend races were infected.
The health scare resonates in Australia where Japanese horses Delta Blues and Pop Rock, who finished first and second in the 2006 Melbourne Cup, are due to enter quarantine here in the next two weeks ahead of November's Cup.
Peter McGauran, Australia's agriculture minister, issued a statement saying Japanese horses should be able to compete in Australia so long as they had not been to a stable, racetrack or other property where infected horses had been identified.
"Equine influenza (EI) is extremely disruptive to horseracing because of the restrictions it places on horse movements required to control the disease," McGauran said.
"EI is highly contagious and can spread rapidly through stables and studs. It has never been present in Australia and poses no human health risks.
"Australia will not take any risks with horses being imported from countries where EI is present.
"There are clearly laid out procedures relating to horses coming into Australia from countries affected by EI. There needs to be at least a two-month gap between when a horse is presented for export, and any possibility of it being exposed to the virus."
McGauran said the Australian government had spent 616 million dollars (491 million US) over the past three years to strengthen quarantine protection.
Racing Victoria Ltd chief executive Stephen Allanson said his office was monitoring the situation.
"We have been speaking to Japan and it seems Pop Rock and Delta Blues have not been exposed to the virus at this stage," Allanson told Monday's The Age newspaper.
"From what we have been told, the outbreak has been discovered in two major training centres.
"They have two weeks before going into quarantine but we will have to wait and see. The final decision will be made by the Australian Quarantine Inspection Services."
Pop Rock is currently the favourite with bookmakers for the Melbourne Cup (3200m/2 miles) at Flemington on November 6.