Hi Pawan,
The JPY currency does not have decimals but is stored in the DB as a decimal value. Check the T-Code OY04 to see if the decimal places has been maintained correctly. Ant conversion exit for amount just converts based on maintenance done here. Then on top of that the rate of exchange is to be considered. Check the link below to understand what are the prerequisites
http://wiki.sdn.sap.com/wiki/display/ERPFI/CURRENCIES+-+Customizing+and+transactions
Cheers,
Arindam