The European Commission says Japan's decision to ban imports of cloven-hoofed animals and meat from all European Union countries appears to be excessive.
Beate Gminder, the commission's spokeswoman for health and consumer protection, says they have made urgent contact with the Japanese.
The Japanese agriculture ministry has said it is extending its ban to all EU countries after foot-and-mouth disease was reported to have spread to Ireland and Holland in addition to the UK and France.
Gminder says: "The measures appear to go beyond what is necessary in the present circumstances."
The commission's agriculture spokesman Gregor Kreuzhuber says the Japanese are large-scale importers of EU pork products.
He says 43% of these imports come from Denmark, where there has so far been no fear of foot-and-mouth disease.
Kreuzhuber states: "I think it's understandable from our point of view that we are concerned because we are not just talking about figures, we are talking about the livelihoods of farmers."
He says he is also concerned that EU trading partners are using the foot-and-mouth outbreak as an excuse to extend protectionist measures to unrelated products.
A threatened ban by Morocco on EU cereal products has been resolved after the authorities in the north African country requested assurances that cereal imports did not come from affected areas.