The Japanese are a civilization with a powerful military but their economy is unique and may take some time getting used to.
The Japanese have a strong emphasis on their military. Their economic system uses shrines to assist in resource gathering. This potentially allows for improved resource production and potentially allow for fewer population slots to be used for economy and more for military. Once they begin to attract wildlife and herd animals, their extensive resource gathering boost will be even more appreciated. One of the Japanese wonders, the Toshogu Shrine, enhances the other shrines and acts as a large shrine itself. Shrines can also receive a boost from the Home City card Heavenly Kami, which increase shrine line of sight and hitpoints, reduces their cost, and increases the amount of resources they generate. This allows for a powerful economy later in the game.
Another unique ability is that many Japanese Home City cards can be sent twice. While they and all Asian civilizations lack the three-villager card, they have the capacity to send the two-villager card twice. This two-sending ability will make for interesting strategies early on, as players weigh their options in the early game. Japan also has an impressive set of mercenary shipments at their disposal, which will often become an important part of many strategies.
Militarily the Japanese can build up an army very quickly. This is mainly due to the Daimyo unit, which can be used to ship units directly to him or to create units like a mobile barracks. The Daimyo is also a tough fighter and provides an attack bonus to nearby units. Their main unit, the Ashigaru, functions as a powerful musketeer. With the right cards and boost from Wonders they can become some of the strongest units in the game.
With the Home City card TEAM Chonindo combined by the Portuguese TEAM Fish Market card, both civilizations can be very difficult to defeat on water maps.
The Japanese economy starts off slowly as they cannot gather food from hunting. Instead they must farm or fish it. However, the player has an additional option of building Shrines, buildings that attract local wildlfe and lead to a steady stream of a certain resource. Enemy players will be unable to hunt animals currently at a shrine and must destroy the shrine first. However this means to gain maximum output from a shrine there needs to be a decent amount of animals nearby, poor placement means a lower resource trickle.