The Japan Racing Association said on Friday it has cancelled horse races this weekend for the first time in 35 years at the Kokura, Niigata and Sapporo race courses in order to prevent the flu from spreading.
The association had initially given the go-ahead for the races Thursday. But on Friday, it said that 29 out of the 163 horses who were to take part in the weekend races were infected.
The JRA prohibited all horses from moving except between the association's facilities.
Meisho Samson was to leave Japan for France next Wednesday with its owner in preparation for the Grade Two race at Longchamp on September 16 before the Prix de l'Arc de Triomphe on October 7.
Even if the prohibition is lifted in time, there is still a possibility that France would refuse to allow the colt in.
Meisho Samson, last year's surprise winner at the Nippon Derby, is one of the main hopes for Japan at this year's Prix de l'Arc de Triomphe.
Last year Japan's Deep Impact came third, failing in expectations he would be the first foreign horse to win Europe's top prize. Deep Impact was later embroiled in a scandal over testing positive for a substance banned in France.
The JRA last halted races in December 1971, barring competition at the Nakayama and Tokyo race courses until February the following year due to the horse flu.