You cannot buy a Japan Rail Pass in Japan. A Rail Pass Exchange Order MUST be purchased outside Japan, prior to your trip.
You then present the Exchange Order at a major station in Japan in order to obtain the actual Rail Pass, which is valid for the designated period (consecutive days).

Who is eligible for the Rail Pass?

Tourists visiting Japan from abroad for sight-seeing, under the entry status of "temporary visitor."
Your passport must be shown at the time of presenting the Exchange order for the Rail Pass, so that your immigration stamp can be checked.
The main Rail Pass for travel throughout Japan can be bought and used by Japanese nationals who can show they have residency abroad. But the Regional Passes, only valid for certain parts of the Japan Rail network, are not available to Japanese nationals, even if they are resident outside Japan.

Rail Pass types and prices

There are two main types of JAPAN RAIL PASS: Green (for superior-class Green cars), and Ordinary. Each of these types is valid for train travel throughout Japan, and is available as a 7-day, 14-day, or 21-day Pass.

The Rail Pass is priced in Japanese Yen (see box above); the actual cost in local currency is calculated at the time the Exchange Order is issued. Note that the purchase exchange rate may differ from the exchange rate in effect when you actually visit Japan.
The local currency price, applicable exchange rate, and issue date for an Exchange Order are specified on the Exchange Order itself.
PASS prices for children apply from age 6 up to and including age 11.
Prices are subject to change.
The applicable price is the price valid on the date when an Exchange Order is issued.
In Japan, present your Exchange Order at any applicable Japan Rail Pass exchange office to receive the actual Pass.

Validity period

The validity period of a JAPAN RAIL PASS is the consecutive 7, 14, or 21 days beginning on the date the Pass is first used.
Within three months from the date the Exchange Order was issued, you must turn in your Exchange Order to obtain your JAPAN RAIL PASS. At that time, you have to specify the date that you want to start using the Pass. It can be any date within one month from the date the PASS is received.
Once the Pass has a starting date written on it, the date cannot be changed.

General tips

Do not use an automatic ticket-reading gate with a Japan Rail Pass . Please show the Pass at a manned ticket gate.
Caution: Please note that during crowded periods you cannot be guaranteed a seat on a specific train. The periods when seat reservations are particularly difficult to secure are as follows.
* December 29 to January 5
The New Year holiday period is the most popular travel time for Japanese people, for vacations and returns to hometown areas.
* April 29 to May 5
Due to consecutive holidays in a comfortable travel season, there is large - scale travel throughout Japan for leisure and recreation.
* August 13 to 15
The "O-bon" season, another traditional time for travel to hometown areas.

Making seat reservations

Shinkansen (Bullet trains) and most Limited Express and Ordinary Express trains have reserved Green Car seats (First class) and both reserved and non-reserved Ordinary Car seats (Standard class).
For a non reserved seat, simply show your Japan Rail Pass to board.
To make a seat reservation, visit any Travel Service Centre or reserved-seat ticket office called "Midori-no-madoguchi" at a Japan Railways station in Japan.
Normally, seat reservations cannot be made from outside Japan.

However, from 25 March JR East have opened their new internet rail seat reservation system. This allows travellers to make advance seat reservations for all JR East Shinkansen (Bullet trains) as well as certain JR East Limited Express trains.
This system allows JR Pass holders, JR East Pass holders and also non-pass holders to make seat reservations.
To make a reservation, travellers have to enroll as a member (sign-up is free). Then check the types of trains and specific times, and reserve seats. Travellers just need to pick up the tickets when they arrive in Japan (at any location specified by East Japan Railway Company within the JR East area).
JR East Shinkansen Reservation website