According to aviation sources, some airlines have already raised the issue with the Civil Aviation Ministry and Airports Authority of India (AAI) in the recent past.
They have stated that they had to pay between Rs 8,000 and Rs 10,000 per landing at several airports where these payments are not permitted according to rules.
The airports include all major metro airports as well as almost two dozen non-metro ones.
In this regard, the sources also quoted AAI's 2014-15 document on 'Charges for Airports and Air Navigation Services'.
The document says: "No landing charges shall be payable in respect of (a) aircraft with a maximum certified capacity of less than 80 seats, being operated by domestic scheduled operators, and (b) helicopters of all types."
The rules are valid for small 70 or 80 seater aircraft like Bombardier Q400s, turbo-prop ATR-72 and Canadian Regional Jets (CRJ-700).
However, the rules also say that for all civil enclaves at defence airports, the payments have to be made to the defence authorities concerned.
Commenting on the issue, Debashish Saha, Council Member of Aeronautical Society of India, said the Ministry should take steps to implement the rules on landing charges, which existed in the AAI's regulations earlier too.
While the airlines were already burdened with high taxes on jet fuel which formed 45 per cent of their total operational costs, such charges, which should not be levied on the airlines operating small aircraft, should be done away with according to existing rules, Saha said.
Such measures would also go a long way to improve air connectivity to non-metro cities, which was a major priority of the NDA government, he said.