Sections 271D and 271E of the Income Tax Act prohibits acceptance or repayment of loan or deposit of more than Rs.20,000/- in cash. As the intention is to check black money it can apply to any transaction between private parties. It is not advisable to transfer cash in front of the Registrar. The Registrar may not even accept that.
Generally in most property transactions part of the money is paid in black. But what is paid by cheque only will be shown in the transfer deed. Also such amount should be reasonable in relation to the market value of the property.
According to me paying the whole amount in cash only is not desirable. That is done mostly in films and TV serials. Also if the buyer of the property is asked to show the source of income for the purchase, what will do? He will have to show corresponding bank transactions. Beyond 6 years one may not be asked to show accounts and bank transactions. But sometimes 6 years can be too long. Also at the time of registration of the deed, both the seller and the purchaser will have to furnish their respective PANs and the transaction with the PAn's would be posted on the internet. It will be available for the income tax department. When they assess the person's income tax return they may view the transactions also. If they suspect, they can call the person to explain.
Hence it is not desirable to pay the whole amount by cash only. Whatever shown in the sale deed should be paid by cheque only.
There is a saying. How to catch a stork? You place a ball of butter on its head. The butter will melt in the sun and blind its eyes. Then go and catch it. Some of the suggestions above are like that.