Property Transfer - Deficient Stamp Duty Notice

Property transfer deed was executed in 2 years back by paying 6% stamp duty as per standard rates based on locality. We got a notice on Nov 11 2020 to pay additional stamp duty of xyz amount. The notice says that the property value is xyz and the stamp duty we need to pay is Rs.xyz. This is near about 10% of the property value which is incorrect. We have already paid the stamp duty of Rs.xyz which is 6% of property value. It is not the case that there is some error in property valuation as the notice is also mentioning same property value. We are asked to reply within 30 days so we went to registrar office but he was not in a position to hear us out and explain us the reason behind the notice. He asked us to visit back after two days. There seems to be miscalculation happening from Department of Stamp duty and Registration office and how can they demand stamp duty of around 10%. Please advice best way to handle this issue as it is creating lot of stress. Sorry I haven't mentioned actual amounts to keep things confidential.