How did samurai warriors weaken Japan's imperial government?

Any time an armed and well-trained militia is allowed to develop a certain degree of independence from the central government, it will invariably grow in strength and eventually threaten that government. Such was the case with the Japanese samurai. These warriors served at the pleasure of a warlord, or shogun, and their loyalties to the shogun grew over time to exceed that directed toward the imperial regime. These fierce, dedicated warriors grew sufficiently in strength so as to pose a direct threat to the rule, if not the legitimacy, of the Emperor.
The samurai could hardly have been considered particularly noble; in a very real sense, they were little more than mercenaries who operated at the whim of wealthy landowners. Their responsibilities, however, did entail serving as an armed guard against outside forces, such as the Mongols, as well as combating armed criminal gangs. Their loose affiliations, however, made them susceptible to exploitation by anyone with money and an agenda. The bottom line, then, is that the samurai enforced edicts set forth by whoever was paying them irrespective of the ramifications for the imperial house. When their employers, say, a particular shogun, wanted to pressure the emperor, the samurai were the instrument of their policy. In this sense, the samurai most definitely weakened the imperial government. This situation would remain until the Meiji Restoration of 1868, which saw a strengthening of the emperor and concomitant weakening of the power of the shoguns.