Dear Pankaj,
It is always confusing to calculate registration charges in pune/ Maharashtra state. I would like to explain you it in a simpler way. In pune (by november 2017) I find only three kinds of payments paid by the property buyers to the govt.
They are Stamp Duty, Registration Charges and Cess.
Stamp duty is 5% of the total salable amount of the property.
Cess is 1% of the salable value of the property.
Registration charge is 1% of the salable value of the property or Rs. 30,000 whatever value you find less.
You can find a detailed explanation in the link provided.
https://www.zippserv.com/pune/blog/stamp-duty-registration-charges-ready-reckoner-rate-flats-land-property-punemaharastra/