You can pay by cash to Governmental agencies, no bar.
As per rule 6DD of the Income Tax Rules 1962, disallowance due to application of Section 40A(3) shall not be made if payment is made to the Government.
So limit of Rs 10,000 shall not apply in case of payment of land revenue to the Government, so you can make the payment in cash or crossed cheque as per your choice.
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