Document registration charges and stamp duty paid in excess

We decided to register " Gift deed to blood relative" with the registrar. We approached a bond writer for the preparation of the gift deed and registration process. For this, we paid him 1% of immovable govt. index value. After registration, we collected a registered document and it reveals that the bond writer paid stamp duty and registration charges which were of a nominal amount. Therefore we asked the bond writer to refund the excess of registration charges paid to him. He is neither denying nor willing to refund since last 15 days. The charges paid to him is by cheque. He delivered the registered document after 1 week. Kindly guide.