Getting Around Japan

http://willerexpress.com/bus/pc/3/top/

WILLER TRAVEL operates the comfortable high end of overnight bus transportation. They recently added a new line of luxury buses that still cost far less than taking a flight or the train.

Suggest you read my post before you make a decision whether to go for the Hakone Free Pass on the Odakyu railway or take the shinkansen to Odawara:-

http://forum.virtualtourist.com/discussion-575647-1-1-Travel-0-977041-Hakone-discussion.html

The main JR pass covering the whole country is well covered on VT, and I won't go into further detail here, but it is less well known that there are a number of regional rail passes.

Depending on where you plan to visit in Japan, a regional rail pass could present a better deal. Here are the various links to the various rail passes available.

Hokkaido Rail Pass

Shikoku 3 day pass (Japanese language link)

Kyushu Rail Pass

Sanyo and Kansai Rail Passes

JR East and Kanto Rail Passes

Finally cheaper air travel within Japan is here.

Peach has launched using Kansai airport as its hub, with flights to Sapporo, Kagoshima, Nagasaki and Fukuoka. They are advertising fares currently around the 4000 yen mark.

There are two other Low Cost Carriers who will start operation soon, and they will use Narita as their hub.

Peach's website is here and I will update this tip when the other lowcost carriers launch.

Peach Airlines

ANA offers a Premium Service on most domestic flights within Japan. When flying out from Tokyo Haneda this includes lounge access, and onboard alcohol is included (usually they charge 500 yen for a can of beer in the economy section). Seat is normal short haul business size. It is usually significantly more expensive than their economy class. A light meal is also included.

JAL offers J class, and the only difference with their economy class is that the seat is slightly bigger, and it costs an extra 1000 yen only most of the time.

ANA Premium Class
JAL J Class

I have used both but 90% of the time I fly economy within Japan.

JAL also offers a first class service, but this is only on a handful of routes, and so I have never used it.

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May be you want to travel inside japan ? Visit other places than TOKYO, OSAKA or KYOTO?
Want to discover HOKKAIDO or enjoy the climate of OKINAWA, you think it's too far from TOKYO or OSAKA and you don't have time.
It's possible to save time with the JAPAN Air Pass.
The JAPAN Air Pass is offered by the two JAPANESE airlines cies ANA and JAL to buy cheaper tickets on domestic routes only for exclusive use by foreign visitors.
The JAPAN Air Pass has to be purchased outside of JAPAN and before you leave for JAPAN.They can only be used by non-résident of JAPAN who arrive and depart from JAPAN by international flights.Some differents types of Air Pass are avalaible, there are some blackout periods during wich Air Pass can't be used.
We used Air Pass last year when we went to HOKKAIDO, from TOKYO to SAPPORO and return from HAKODATE to TOKYO, the price was 10000.yens per flight for 1 person, not expensive considering the distance traveled and time saving.

Thanks everyone! One more query - I intend to reserve seats on my JR pass. I understand you do the reservation at the JR office. How long should I allow for the reservation before the departure time eg if a train is leaving at 11, when should I get to JR office? Alternatively, if I am confident about a certain train time, should I book in advance when I'm near a JR office that looks pretty empty?

Part of the experience travelers to Japan look forward to is a ride on the Shinkansen (Bullet Train). The Tokaido Shinkansen line from Tokyo to Kyoto is probably the most traveled route, but many people forget the other option - airplane. At almost 3 hours the Tokyo/Kyoto route can be enjoyable one way but a bore both ways. From Itami airport in Osaka it is possible to fly to Haneda in Tokyo in under an hour. Check in is fast an efficient, often taking no more than 10 minutes, including security. The cost of a flight is usually equal to the train and can often be less, especially when booked from outside of Japan.
Check the domestic budget carriers like Skymark, or the more luxurious Starflyer.
Certainly any domestic trip in Japan to the far North (Hokkaido, Tohoku) or the South (Chugoku and beyond) is more comfortable and cost efficient by air.