Issues concerning food quality and safety are becoming ever more important with, for example, risks from BSE and genetic engineering. To better understand how such issues can affect food supply system in Japan, the author investigated the effects of an outbreak of avian influenza which occurred at an egg farm in Ato town, near Yamaguchi city, Yamaguchi prefecture, in January 2004. The author tried to find out the effects of the outbreak on the supply system of local eggs and chicken and also interviewed twice, in September 2004 and September 2005, ten supermarkets in Yamaguchi city to find out what countermeasures they took after the outbreak. The author also assessed the recovery of the supply system and discusses effective means to clarify the characteristics of today's food supply system under the growing interests of food quality and food security. The main findings were: (1) The outbreak had a considerable impact on the supply system. Many supermarkets reported a drop of 20% to 30%, and some a drop of 50%, in sales of chicken and eggs for several months. (2) Few supermarkets reduced how many chicken and eggs they procured or the selling prices. Most supermarkets tried to convince their customers that their commodities were safe by tracing their sources for a short time. Some supermarkets began to obtain their commodities from farms outside Ato town or even outside Yamaguchi prefecture, even though their original suppliers had not been infected, perhaps in response to rumors. In contrast, one and a half years after the outbreak, the supermarkets mainly obtained eggs and chicken from farms in Yamaguchi prefecture again, but they were constructing multiple procurement channels. (3) The countermeasures reflect the growing importance of supermarkets being able to keep their image as providers of safe food. The countermeasures are therefore part of risk management. This survey revealed that the perceived threat of unsafe food was greater than the real threat. In fact, though no unsafe chicken or eggs were found in any food store in Yamaguchi city, the impact of the outbreak upon the supply system was quite large, with consumers becoming hesitant to buy chicken and eggs. An association of the chicken industry of Yamaguchi prefecture said that consumers did not have enough accurate knowledge about the egg supply system, and they obtained information about food safety only through the mass media. This shows that perceptions of food quality can have a greater impact than the real quality on the food supply system, and can trigger the need to quickly form a new supply system. From a geographical viewpoint, compared with the supply and distribution systems that depend on large-scale production and consumption, double-linear or multiple style networks may help reduce the impact of safety threats, real or perceived. We also should pay attention to dissemination of geographical information about the food source.