"We will do everything under the legal framework," said Road Secretary Vijay Chibber.
There were reports that the law ministry overturned a decision of the National Highways Authority of India (NHAI) to allow road companies to collect toll from highway users first and pay the authority later.
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NHAI had earlier allowed GMR to make payments of Rs 32,508 crore so that the company would pay less in the initial years of the concession period and higher sums later, while keeping the net present value of the premium unchanged.
In an e-mailed response, a GMR spokesperson said: "We have not received any communication from the ministry in this regard, and hence we are unable to comment."
The Planning Commission, in its observation, had said any change would mean all the contracts would be open to review and renegotiation.
The projects of GMR, GVK and IRB involve six-laning and toll collection starts from the four-lane stage. Spreading the premium over the concession period helps companies by reducing their cash outgo in the initial years when they have to spend on the construction of the roads.