Although the area I live is far from rural, there is also a lot o effort to use locally produced food as well. We receive monthly notices discussing the food used in the lunches and various other tidbits about the lunches and they always stresss the use of Kanagawa prefecture grown produce (this is the prefecture Yokohama is located in).
I know no systems are perfect, but I think the school lunch systems in Japan are among the best that you can think of, especially those in rural areas like my town, where locally grown safe farm products are used whenever possible. (This is rather off-topic, but a lot of efforts are being made in Japan these days toward "jisan jisho" 地産地消, or "local production for local consumption", and these efforts are compatible with the need for safe farm products for use in school lunches.)
Sleepy Dragon mentioned that he liked the idea of the kids serving it themselves as it shows that they are not above such work, you should also know the children are responsible for cleaning the school as well, including hallways and toilets. This is also part of their education. All of the work done around the school is done my te kids (with the teachers) or by the parents. The parents help put up and take down decorations, plant flowers, clean up the yard, etc