Notably, the Northeast has several toll gates including three in Assam and one at Byrnihat in Meghalaya.
The country has been put under a complete lockdown for 21 days till April 14 next.
All air, rail and road transportation services have been suspended.
In a tweet, Nitin Gadkari said maintenance of roads and the availability of emergency resources at toll plaza will continue as usual.
He said that the move to suspend toll collection was to reduce inconvenience to the supply of emergency services.
On Tuesday, the MHA issued an order detailing guidelines for the nationwide lockdown.
As per the order, all offices of the government barring for those providing essential services will remain shut.
They will function with a minimum number of employees.
Hospitals and all medical establishments will be open and the transport of the people working in this field will be permitted.
All commercial establishments and private organizations will be closed.
The exemptions include print and electronic media, shops selling essential items, e-delivery of food, medical equipment, banks, petrol pumps etc.
The suspension of transport and hospitality services shall continue.
Moreover, legal action can be taken against a person who does not follow the quarantine period prescribed by local health authorities.