It depends on what contract you're on and the residency status. I'm on the A-Net contract. We're categorized as "temporary residents" which is for people who will live here for less than 5 years. As a temporary resident I've paid 8% tax on my salary minus a basic deduction that everybody gets. If you're on the Air Japan contract I don't think you pay Japanese tax as you don't get a Japanese working visa. I don't know about the other contracts.
bg