Well, at least, three lucky people will every year according to the article at ANN. To quote from the article:
The Japan Image Council (JAPIC) and the Japanese Agency for Cultural Affairs have launched the Animation Artist in Residence program, which will offer three applicants room and board for 75 days in Tokyo for education, training, and workshops, with the goal of creating all or part of a new work by the end of their stay. The program is open to all participants ages 20-35 who have screened at least one work at any international film festival, are from a country other than Japan, and speak Japanese or English well enough to get by in Tokyo. The deadline for applications is September 10, 2010, and the program itself will run for 75 days between January and March 2011. Successful applicants will be provided with travel and living expenses, as well as opportunities to interact with Japanese creators.
There is also a program for younger animators in place but if you really want to learn animation, you can also try going to one of the universities in Japan and enroll in their summer animation course for a fee. Tourist visas in Japan last for three months so you can also easily extend your stay after your summer course is completed and take a vacation.