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.
The samurai were Japanese warriors who came to true prominence in the 12th century CE. Governed by a rigid sense of honor, samurai served a master or lord (called a daimyo) and served as the elite military force within the country. In the 12th century, the emperor's power began to decline as local lords and leaders claimed more power and exercised more authority, as it was ultimately the daimyos, and not the emperor, who commanded the loyalty of the samurai. While the emperor and his court no doubt objected to this unauthorized decentralization of authority, there was, in fact, little that could be done. If the emperor had wanted to challenge his rebellious lords on the battlefield, he needed the help of the samurai, and the samurai were more likely to help their daimyo than the emperor. In this way, the samurai weakened the central government during the height of their power.