The More respected ones:

Sengoku - available in a fusion system and Active Exploits (diceless) version. Named for it's setting: Sengoku period.

The Blossoms are Falling for use with The Burning Wheel RPG. Set in the Heian period

Legend of the Five Rings is in it's 4th edtion, but some 2nd and most 3rd edition books are still available readily. The setting, Rokugan (literally Green Rock and 5 rock), is vaguely Shogunate, but integrates also Chinese and Korean elements, as well as moving from being on islands to being on the mainland in a position comparable to China.

GURPS Japan An excellent multi-era sourcebook for both historic and low-fantasy Japan. Many elements useable with non-GURPS RPGs as well. Covers from 12th C to the Meiji Restoration. Definitely the right book for GURPS fans.

Less well respected but still worthy:

D20 Oriental Adventures adds more southeast Asian and Chinese monsters, and also includes the basics of the Legend of the Five Rings setting, called Rokugan. More details are added in additional books. If you like D&D 3E or 3.5E, or any other d20 system games, this may be a good choice.

AD&D 1E Oriental Adventures is an ecclectic mix of Japanese, Chinese, and Korean elements, in a setting named Kara-Tur. Pretty close to standard AD&D 1 mechanics, but includes the presumption that non-weapon proficiencies will be used, and includes rules for using them. Interesting, but not well supported, and very much not focused on realism. Only available 2nd-hand. If you like AD&D, this is your best bet.

Bushido is one of the oldest of the games on this list. Still, it's quite servicable, and is still available in PDF. The setting material is Shogunate era fantasy Japan. It has one of the best visual aides to Japanese weapons in gaming. The system is quite playable, but the setting materials (aside from monsters) is pretty thin, tho actually impressive for its era of initial publication.

Blood and Honor is a very narrativist system focused on Japanese roleplay, but it isn't very much for the setting aids. (It in fact recommends several of the above.) What it does do is provide for mechanical narrativist resolution emulating the Japanese Pillow-book genre, which is itself originating in the Heian era... It can easily be used for both historical and low fantasy games, as well as no-magician-PC mid-to-high fantasy samurai games.

Usagi Yojimbo - both in Fuzion engine and a custom one by Sanguine Productions. Based upon the comic of the same name, these are both fairly well researched. While the characters are anthropomorphic animals, the setting info is pretty pure shogunate era.

A few more good ones I don't recommend, and why.

Land of Ninja is for Chaosium's RuneQuest RPG. I don't recommend it solely by lack of knowledge - I've never handled an un-shrinkwrapped copy.

Ninja Hero for 5E Hero System. Another "I don't know this one well enough to recommend it." I can say that in 5E, it's not the Martial Arts book; that's a separate book.

Ninja Hero for 4E - while an excellent supplement, it is not really about Japan. It is really the Martial Arts supplement for 4E Hero system, and has a few setting elements drawn from both chanbarra and anime traditions, but isn't primarily a setting book; the setting is just an excuse to use the martial arts included, and they are the majority of the book.

Magic in the above

All of the above have some forms of magic. Yes, even Blood and Honor, tho it lacks any spellcasters. L5R, OA, and Bushido have powerful spellcasters; Sengoku has less so, but still chanbarra level. GURPS Japan, and Land of Ninja use the extant magic systems for their respective systems; Ninja Hero uses the superpowers system for the chanbarra style magic users.