Motorists who converted their cars to use environmentally friendlier fuels to avoid paying the congestion charge could lose their exemption.
The discount will be phased out by 2010
Transport for London (TfL) has announced plans to phase-out the Alternative Fuel Discount (AFD).
But the move would only affect a "very small number of car owners," a TfL spokesman said.
Vehicles running on fuels such as liquefied petroleum gas (LPG) will be affected by the proposed change.
TfL plans to stop offering the 100% discount completely by 2010 and will not offer the AFD to new registrations.
Highest polluting cars
The announcement is part of plans to charge £25 for the highest polluting cars entering central London zone.
Michael Jameson, from Victoria, central London, paid £2,000 to convert his Hyundai Trajet 2.0 petrol car to run on LPG in September 2003.
He has discovered that he may now be forced to pay to travel in the congestion zone.
"It looks like I will have to pay the £25 per day charge because if my car ran on petrol it would be above their threshold, slightly," he said.
"But, as it runs on LPG at a considerably lower CO2 level it should be still exempt.
"It's totally unjust. How does this encourage people to be green?"
A TfL spokesman said: "A very small number of car owners will go from qualifying for a 100% AFD to falling into the £25 a day CO2 charge bracket.
"That is why the AFD will not be phased out for almost two years, giving owners time to change their vehicle."
He added vehicles converted to use LPG can still use petrol, which is associated with CO2 emissions.