Provided courtesy of Tokyo Itabashi City Hall: 

Workmen’s Compensation Insurance for Accidents (Rosai Hoken)

If you are injured, become ill due to work, die from overwork (karoshi), commit suicide due to excessive work, or are injured while commuting to and from work and fulfill certain conditions, you may be eligible to receive medical treatment benefits (iryo hosho kyufu), benefits for sick leave (kyugyo hosho kyufu), or disability benefits (shogai hosho kyufu).

This system applies to all foreign workers.

(Inquiries should be made at the Labor Standards Inspection Office for the district of your place of employment.)

By law, all Japanese companies must be subscribed this insurance, although many unscrupulous employers attempt to evade the law by such schemes as classifying their employees as private contractors or subcontractors, or simply by claiming that the law does not apply to foreign workers. Rosai Hoken covers every worker employed in the company, including all part-time, dispatched, and temporary workers, regardless of their residential or visa status.

Responsibility for enrollment and payment of premiums are your employer’s responsibilities: they cannot deduct the cost of being in the system from your salary. If your company does not follow the proper procedures, consult the Labour Standards Inspection Office (Rodo Kijun Kantokusho) in that has jurisdiction in your company’s area.

Remember that it is not your company, but the Labour Standards Inspection Office that is responsible for deciding the validity of your claim.