How might an empire such as japan be hard to defend

At the height of the Japanese Empire, it had spread over countless small islands in the Pacific, as well as several thousands of square miles in Southeast Asia, China and Korea. It would be difficult to defend for a multitude of reasons, one of the foremost of which would be communication over distance. The Japanese Empire was at its height at a time before the invention of wireless communication via satellites and towers, so information had to be delivered via either transmission through telegraph wires (in the latter years of the Japanese Empire) or by direct communication, both of which required extensive networks.
Also, there was the issue of one man trying to maintain the morale of several million individuals across almost a tenth of the globe. 
In addition, keeping supplies well-distributed was a problem.
All of these little pieces work together to create havoc when you are trying to defend a huge empire like that.