[1]http://www.nytimes.com/1988/03/06/weekinreview/the-world-jap...
[2]https://books.google.com/books?id=lfAu0Tl0018C&pg=PA105&lpg=...
It's also probably due to the mentality that producers want specific kinds of potatoes for specific purposes and maybe only trust Japanese farmers to make the specific kind of potatoes the way they want them.
Wasn't sure if it was a strange form of nationalism, or a veiled lobbying effort by an interest group (the abundance of very small scale farmers across the countryside)
Much like energy. When everything is going rosy, relying on high % imports can be economically beneficial. In the case of extreme events like local or global wars, it leaves the country extremely fragile. Even outside wars, if there are drastic price increases in the global market then you are highly exposed. Look at OPEC, the power they wield and how they direct their efforts in essentially geo-political 'battles'.
I don't know much about it, but I suspect that energy and agricultural self-sufficiency are very important and underestimated factors in (developed) nation state security.
So it's a legitimate concern many nation's have, even EU countries have similar programs.
In the US it has gotten out of hand, however.
But people actually campaigning for it...
People, who rarely get worked up about anything that doesn't put money in their pocket or stroke their ego, giving enough of a damn to go out and campaign for it... well, OP said it directly: he wasn't sure whether it was about putting money in their pocket, or stroking their ego.
The apparent bias against resorting to importation also seems to indicate it is largely thinly-veiled protectionism and political cultivation of special interests.
Furthermore however intuitive it may seem it runs contrary to hundreds of years of economic orthodoxy, known as Ricardo's Comparative Advantage.
As with most things, it comes down to a trade-off: increased risk of disruptions from ecological events in return for a decreased risk from geopolitical situations. One is not inherently better than the other, but Japan has a preference for self-sufficiency as much as possible.
How so? Food security is being able to feed the country even when it's completely isolated, not having potato chips on store shelves.
Without protectionist regulation and subsidies European and American farming isn't competitive either.
http://www.npr.org/templates/story/story.php?storyId=6256274
(And if so, maybe one day will be thankful for those barriers and the genetic diversity they facilitate/protect.)