In James Clavell's novel Shogun its stated that the only punishment for breaking the law was death.
As a contrapositive, a fairly common punishment was exile, as well as the stripping of one's rank and income. For instance, Yoshida Shoin, considered to be one of the main progenitors of bushido, offended his daimyo by leaving the territory without permission. As punishment, he lost his bushi rank and income, and was kicked out of the domain for 10 years.