Our North Asia correspondent Shane McLeod reports from Tokyo, Australia's horse flu outbreak is being cited as one of the reasons for the decision.
The nationwide outbreak of horse flu that has swept Japan has made it near impossible for the connections of Delta Blues and Pop Rock to find a location for the horses to complete pre-departure quarantine.
Trainer Katsuhiko Sumii says that factor, along with difficulty finding a cargo plane and uncertainty surrounding Australia's own horse flu outbreak, have led to the decision not to send the horses.
"If they were to be infected in Australia, they would not be able to come back to Japan, and take part in races here," he says.
Mr Sumii says the horses were both in good condition, and he is disappointed they are not able to return to Australia for this year's race.
Australian equine flu spreads to racecourses
In eastern Australia, the horse flu epidemic may have spread to racecourses, with three thoroughbreds at Sydney's Randwick racehorse developing symptoms.
The outbreak is believed to have begun at a property in the Hunter Valley in New South Wales.
The deepening horse flu epidemic has put a cloud over the Sydney and Melbourne spring racing festivals.
There are now 47 confirmed cases of the H3 influenza in New South Wales, and up to 200 suspected cases.
Prior to Monday it was believed that only recreational horses were affected.
But Peter Vlandys, from Racing New South Wales, says three horses at Sydney's Randwick racecourse are being tested because of higher-than-normal body temperatures.
"With the current situation we aren't prepared to take any risk whatsoever. So we've stopped all trackwork at randwick," he says.
The situation has placed in further jeapordy the Sydney Spring Racing Carnival.
The primary industries minister in the south-eastern state of New South Wales, Ian MacDonald is urging horse owners and trainers to comply with the ban on horse travel.
"There are substantial fines if people are to move horses and indeed imprisonment," he says.
He is expected to announce on Monday a further 72-hour extension of the racing ban in the state.