is it necessary to get a reference letter from the place I work to re enter japan while i am on working visa? cause Iam going to my home Country.
As of July 2012, if you wish to leave Japan for a under a year, you can pick up a "Special Re-entry Permit" at the airport just before the immigration desks:
Simply fill in the departure part, and present it with your passport and residence card at the immigration desk. The immigration officer will staple the "arrival" part to your passport, and you should fill this in for when you re-enter Japan.
See here for more information, and any conditions, etc.
Note that there are other images floating around for "special re-entry permit", but this is the only card I've ever actually seen at the airport.
According to http://www.immi-moj.go.jp/english/tetuduki/kanri/shyorui/06.html, if you are applying personally only the following documents are required:
Passport and residence card (or alien registration certificate deemed equivalent to a residence card)