The samurai, particularly the higher-ranking ones, weakened Japan’s imperial government because they were the source of military and even economic power in Japan’s feudal system.
In feudal systems, the monarch or other ruler depends to a great degree on those lower down the feudal ladder. In Japan, the emperors depended upon the samurai for military power. They also depended on the lower samurai to keep the economy running. This meant that some of the higher samurai (the daimyo in particular) were very important. These men would typically try to take as much power as they could. When they did, they weakened the imperial government and effectively divided Japan into a patchwork of provinces ruled by local daimyo and not truly subordinate to the central government.