Visas

The visa problem is definitely the most difficult hurdle that most foreigners have to face when wanting to  work in the Japanese anime and manga industries.

The best source of visa information I have found on the Web is the Consulate General of Japan in San Francisco. Their visa page has very detailed information.

Nakai Immigration Service has a good page dealing with visas and immigration to Japan and they provide services to help people.

WADA Legal Administrative & Translation Services can help you with immigration and visa problems, establishment of companies or branch offices in Japan, and other legal and administrative matters.

Sugaya Immigration Service provides professional and cost-effective assistance with immigration and naturalization procedures.

The Hasegawa Law Office has a great resource page (unfortunately only in Japanese.)

The big question: How many foreigners are in Japan working in the traditional animation (anime) or manga industry with working visas?

None.

The immigration office steadfastly refuses to issue a working visa to anybody working in the traditional animation industry. Animation is seen as a non-essential field and it is impossible to convince the authorities otherwise.

With this in mind, there are other options for someone who still wants to work in the industry.

Note: the following presupposes that the individual has animation training.
Methods for a foreigner to work in the anime/manga industry
Method Plus Minus
Get a job with a very large animation company like
 Studio Ghibli, Toei or Nippon Animation		 It is possible that a large and powerful company could get a working visa for someone with strong skills. Unless the individual has very good skills, better than a good Japanese candidate and excellent communication skills, they are highly unlikely to be hired.
Work as an English teacher and moonlight at an anime
company		 An English conversation school provides a working visa and the hours tend to be short so if you can effectively hide the fact that you are working somewhere else then this may work. See section on English conversation teaching. 
Work at another job and moonlight at an anime company If a job which provides a visa can be found and you can find a way to work both then this could work. The company which provides the visa to you may terminate you if they find you are working another job. If you are terminated for this it is unlikely you will be able to get another visa.
Attend a language school and moonlight at an anime
  company		 Japanese language schools provide cultural studies visas to students which last up to two years. It is illegal to work over part-time with this visa.
Come on the no-visa plan as a tourist and work at a studio Depending on the agreements the individual's government has with Japan, they can stay up to 90 days with no visa. Working on a tourist visa is illegal and if you are caught you can be imprisoned, fined and will be expulsed from Japan and not allowed to return.
Attend school at a university on a student visa and work on the side. Some schools allow students to work a limited number of hours per month. Anime is very much a full time job and can suck important study time away.
Marry a Japanese national. The spouse of a Japanese national can do any sort of work. You need to find a Japanese spouse.
I've been told that the guidelines for the issuance of a business visa are as follows:
  • Company must have over 150 employees. (Only 5 animation studios in Japan do.)
  • The company's net worth must be worth over  one million dollars.
  • The foreigner's salary must be over 250,000 yen per month. (Good luck getting that in the anime industry!)
  • The foreigner must perform a job no Japanese employee can. 
The last one is the real mountain to overcome. Designers, directors and some computer operators might fall into a different category however. The most difficult part of this is that the jobs that would allow a foreigner to get a visa are the ones that require the most experience and would also be the least likely jobs that a Japanese animation studio would let a foreigner do.

In order to get a visa of any type, the applicant needs to have a guarantor (hoshounin). This is a person, preferably a person of some means or a good sized company, who will guarantee that the visa applicant will be taken care of in the case of any problems and who will supervise the applicant so he/she does not go out of control. A friend is usually not enough for the immigration authorities. They prefer a company, a person with reasonable social standing, an employer, a family or a spouse. (In about that order.) (Perhaps a good rule of thumb would be to say that the kind of person who could become a Notary Public in the U.S. could be a guarantor.) For a work visa the applicant must have the employer as the guarantor. A spouse visa does not require the spouse to be a guarantor. 
Cost of visas is 6,000 yen for the visa or extension permit no matter what the length of time. Period of stay varies per visa and is usually six (6) months for a cultural, one year for an English teacher or a working and 3 years for a spouse and some workings. This period can be extended with a Extension Permit available from the immigration office with another stack of paperwork. The Extension Permit is usually the hardest part. There are limits on some visas, such as the 2 year limit on Japanese language study visas. The exact length of extension is determined by the immigration inspectors and there are sometimes changes in policy dealing with what length is reasonable so nothing is sure. If the applicant has not done anything out of line and continues to show a need for the visa then extension usually is granted.
Paperwork that needs to be submitted includes school records and work evaluations and such so if a student is getting poor grades or a worker is having problems then the Extension might not be granted. (Don't skip school to go shopping for anime stuff!) The applicant also needs to provide tax payment records, spouse's employment, tax and citizenship papers and sometimes another letter from the guarantor stating that the guarantee is continuing.
Change permits are also available in some situations. For example if somebody on a student visa was to get married then they could change to a spouse visa. Tourist visas cannot be changed or extended. These are applied for at the immigration office like any extension or visa and require the same paperwork.
Becoming a citizen of Japan is virtually impossible unless extreme circumstances exist so I will not discuss it here. (You would have to be insane to want to live in Japan for the rest of your life anyway...)

Illegal Activities: If you overstay your visa period you can get into serious trouble. At the very least they will kick you out and deny you entrance to the country again. If they catch you working on a tourist "no-visa" they will usually only deport you forever but they can stick you with some serious prison time if they feel like it and fine you the equivalent of the GNP of a small country to boot. Take note Americans - you don't have any real rights outside the US and it isn't like Midnight Express or Rambo - nobody is going to save you if you mess up really badly.
Needless to say, the immigration office is under intense pressure to make sure only "reasonable" foreigners are staying in the country. Japan is crowded and overloaded and unless there is really something unique and important that the applicant can contribute then a long stay will be difficult. The immigration people are not being racist or cruel - It makes a lot of sense to want to control access to a tiny island with a hundred twenty million people on it.

Perhaps it is best to think of it this way: The Japanese are much stricter than most countries about the issuance of visas, especially for frivolous reasons. The equivalent of the US Green Card is very difficult to acquire and takes a minimum of 5 years to be eligible to apply for.