The apex court said that the one per cent amount, charged as environment protection charge, shall be paid with Central Pollution Control Board (CPCB) which will open a separate account with a scheduled public sector bank.
The direction modifying its December 16, 2015 order came on a plea of automobile giants.
The apex court said that the registration of the vehicle would be done by the Regional Transport Officer on the satisfaction that one per cent of the cost of the vehicle has been deposited with the CPCB by the vehicle manufacturers/dealer/sub-dealer.
The bench also comprising justices A K Sikri and R Banumathi said it will decide later whether green cess can be levied on diesel vehicles of below 2000cc engine capacity.
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The apex court had earlier agreed to hear today the plea of luxury car maker Mercedes-Benz offering to pay one per cent environment cess in a bid to overcome the ban on registration of vehicles with engine capacity of 2000 cc or more in Delhi and NCR.
On July 4, the court had reserved its verdict on pleas seeking modification of its order banning registration of diesel-run SUVs and high-end cars with engine capacity of 2000 cc and above in Delhi and NCR, indicating that such vehicles may be allowed to be registered again on payment of one per cent of ex-showroom price as green cess.
Earlier, on June 29, the court had said it was open to lifting the ban on registration of heavy diesel vehicles in Delhi and NCR subject to a levy of one-time environment compensation cess.