The Japanese are primarily an offensive civilization geared towards infantry. The Japanese work well on land maps but fare much better on maps with large bodies of water since it is the only type of map where their bonus on Fishing Ships can be used effectively.
Their infantry attack faster than those of other civilizations giving their infantry an edge in large battles. The Japanese unique unit is the Samurai, a formidable infantry unit that has a fast attack and attack bonus versus other unique units. This is a big advantage in the late game when most civilizations rely heavily on their unique units. Civilizations that rely on infantry units will also be at a disadvantage against the Japanese due to the faster attack speed of Japanese infantry. They also have an effective navy, with fishing ships gaining extra hitpoints and their Galleons gaining more line of sight. They lack the Demolition Ship, but this need not be a negative since the resources would be better spent on Galleons or Fishing Ships.
In contrast to their infantry they have fairly weak cavalry, missing the Paladin and Hussar upgrades. This is in addition to not having the Camel. They also lack the Bloodlines upgrade, putting them at a disadvantage in cavalry battles. The fact that their Spearman have a faster attack and can kill cavalry units even faster than normal somewhat makes up for this but they still lack the speed of the Camel so are less effective when chasing fleeing cavalry. Their siege weapons are also average since they lack the Siege Onager and Siege Ram.
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