Indian rupee number format is different from US number format. e.g. 1,00,00,00,000 http://en.wikipedia.org/wiki/Indian_rupee
How do I setup a custom number format in Numbers?
In Numbers '09, once in the Custom Number Format dialog, drag a few integer elements into the format box. Pull the menu down for each, and choose Hide separator. On the appropriate groups, change the number of digits to two.
If you're not mixing with USD and prefer India's conventions, a much simpler approach is in the Language & Text panel of System Preferences. Choose India from the Region menu, and any cells set to Currency format will not only have the correct symbol, but the correct groupings. Of course, then if you want USD formatted correctly, you'd need a custom format for that - so use whichever region is most appropriate to the bulk of your content.