Stamp duty is payable on circle rate or sales consideration whichever is higher. In your case as mentioned by you that buyer paid stamp duty on circle rate which means sales consideration is less than circle rate. If the difference between circle rate and sales consideration is more than 10% then circle rate would be considered as full sales consideration unless supported by genuine facts for the cause of difference. Also buyer would be liable to liable to pay the tax on the difference.
1. Check from which date new circle rates are effective. You can put your facts before stamp authority that 5% of the sales consideration was paid on the date of agreement therefore value on the date of agreement should be considered for payment of stamp duty and the stamp duty has actually been paid
2. By paying the difference amount
For detailed discussion you may opt for phone consultation