Japan's plan confirms the fears of farmers in the Netherlands, Europe's second biggest poultry producer after France, about possible trade restrictions from countries whose consumers shun meat from vaccinated animals because of possible health risks.
Benno Briggink, spokesman for the ministry, said: "The Japanese chief veterinary official asked us for clarification whether we are vaccinating hobby or commercial poultry.
"They haven't imposed a ban yet, but they say they will do so when we start vaccinating commercial poultry."
He said Switzerland had also asked for clarification on vaccination plans.
The Netherlands, a leading world poultry exporter, plans to launch vaccination of its 1 to 3 million backyard poultry and about 5 million free range poultry in about 10 days after receiving a green light from the European Union earlier this week.
Dutch farmers have said they will reject vaccination if they are not able to export.
Preventive vaccination will be voluntary throughout the country and an alternative to the requirement that birds be kept indoors to avoid contact with wild birds infected with the H5N1 avian flu strain.
The Dutch government fears a repeat of the devastating 2003 outbreak of a different bird flu type that led to the culling of 30 million chickens, and says vaccination could limit the spread of the disease.
EU member Britain has taken a strong stand against the use of vaccines, saying they could hide the disease. The EU has been split on the merits of preventive vaccination against animal diseases, especially since it can damage trade.
Supporters of vaccination argue the benefits outweigh the risks and see the measure as an antidote to slumping poultry prices.