The authorities say the loss over the last two days is around Rs 65-70 lakh.
The call for protest was made by over two dozen groups from Noida, forming the "Janhit Morcha".
Since Sunday morning, hundreds of them have been camped near the toll plaza and the DND office, demanding that the plaza be made toll-free and an inquiry be set up to check the alleged financial irregularities. They forced the toll bridge employees out of their posts and let the vehicles pass through without paying.
City magistrate Bachu Singh has said they were "trying to have a settlement with Janhit Morcha" and doing their best to "end the protest end as soon as possible".
Claiming the protest was against corruption, Mr Nagar, a former UP minister had said the Noida toll bridge company had spent Rs 183 crore for its construction.
The company, he said, claimed they used over Rs 400 crore, but even that cost has been covered. "Now they are just continuing to loot people," he had told NDTV.
The court has issued a notice to DND flyway authorities but no order had been passed yet.
Detailing the terms of agreement of the flyway, a DND spokesperson said, "DND's Concession Agreement with NOIDA is for a period of 30 years, that is till 2031, which is not unlike other National Highways Authority Of India or NHAI concessions. Such activities cause concern among investors about public money/investments in PPP projects and the infrastructure sector in the state/country."
She said the company is a privately owned and has over 80,000 shareholders.
The expressway, operational since 2001, considerably reduces the travel time between Delhi and Noida. At present, Rs 30 is collected as toll from each vehicle. On an average one and a half lakh vehicles use the route.