Hey, glad I came across this question, since the guy who wrote the article on this topic (Thomas Nelson) happens to be my mentor. It's a pretty great read that you can look up on JSTOR (literally just called "Slavery in Medieval Japan"), but the short answer is, it definitely existed, and was well-recorded in both Japanese and European sources. Most prisoners came from POWs either from in-fighting or in the Korean War. One Italian guy who visited Japan in 1598 - 99 mentioned there were a great number of slaves available for very low prices, fresh from the Korean invasion. Slaves had no rights, and could be killed by their masters any time they wanted to. Some people sold themselves or their children into slavery; I believe there are some literature on this topic as well. In fact, one of the reasons Hideyoshi gave to ban the Europeans was that they were engaged in the slave trade, although it was obvious the Japanese themselves practiced it too (one contemporary European complained that while it's true some Portuguese merchants bought cheap slaves to take back home, this is only possible at all because the Japanese were willing to sell).

This was a phenomena that continued into the early Edo period; in 1613 Vizcaino (a Spanish visitor) was still saying that Japanese people are willing to sell their wives or children. Also possible it continued later, but here my expertise dwindles out somewhat.