I presume you mean during the Edo- or Tokugawa-period? My old, Finnish, high school schoolbook, Kaikkien aikojen historia 6: Kulttuurien kohtaaminen, says that it was mainly to stop foreign ideas, like Christianity, from spreading. In 1590, Toyotomi Hideyoshi, who had conquered nearly all of Japan by that point, thought that Christianity, and nobles converted to Christianity, was a threat, and oppressed Christians. In the early Tokugawa-period, there was a number of Christian revolts in Japan, which might have affected the decision to isolate Japan from the world.

Foreigners were greatly destabilizing the political and military situation in Japan. At the time Europeans first arrived in Japan in significant numbers in the 16th century, Europe was undergoing an age of exploration and also having religious wars. Those who landed in Japan were looking for allies, for countries to conquer, and places where they could spread their version of Christianity. Consequently, Europeans made alliances with various feudal lords and provided them with weapons that had no equivalent in Japan. They converted feudal lords, who in turn converted all of the people under them.

While this was going on, Japan was itself in turmoil. The Shogunate that had previously ruled Japan had lost power and a whole bunch of different feudal lords were fighting and seeking alliances with other feudal lords in order to unite Japan under one ruler--a shogun. The weapons and promised trading and power associated with allying with European states made the situation more complex. It could turn someone with few resources into a major power. When Tokugawa Ieyasu finally succeeded in uniting Japan about around 1600, ushering in the Edo Period and spawning a line of Shoguns who ruled Japan until the mid 1800s, he wanted to prevent other lords from challenging his power. And he was both paranoid and wise in preventing this. By making contact with other nations severely limited, by outlawing guns, by outlawing Christianity, they were able to exert more of a stranglehold on power. They continued to allow trade with the Dutch, because the Dutch were only interested in trade--not in the religious wars of the Spanish, Portuguese, and English, for example.