The permission to pass through the ghat section was given after the company deposited Rs 20 lakh as compensation to the road authorities.
The proposed 13km-flyover will be constructed between Aroor and Thuravur in the Alappuzha district, said Union Minister Nitin Gadkari.
Protests had erupted after the highway stayed closed to commuters despite its construction being complete.
The NHAI gave the clarrification as a reply to an RTI query posed by KPCC secretary Shaju Kodankathu.
A number of birds, mainly cormorants belonging to the Schedule IV of the Wildlife Protection Act, were killed in the incident.
Even as the contract provides for carrying out road resurfacing works once in five years in all the National Highway stretches where tolls are collected, the same is not followed in Kerala.
The accident happened in front of the famed theatre company Kerala People's Arts Club.
The police have registered a case against the National Highway authorities and the contractor after a Manjali native riding a bike died after falling into a pothole at Nedumbassery along the Edapally-Mannuthi (NH 544) stretch.
The total number of fatal accidents in 2020 is 12.23 per cent lower than the 2019 figure of 1,37,689.
In all seven panic-stricken horses ran out of the stable of nearby private horse-riding academy apparently after hearing the trumpet of elephants.