Bernd Gottschalk, president of the Verband der Automobilindustrie (Association of the Automobile Industry), said the changes could damage new car sales and prevent the economic upswing thatautomakers are anticipating.
"It is a questionable concept at the wrong time," he said.
Manfred Schoch, chairman of the BMW Group's general works council, said the new tax regime could lead to job losses.
The German Federal Environmental Protection Agency (UBA) plans a new road tax formula based on a vehicle's CO2 emissions instead of engine size.
Axel Friedrich, the UBA environment and traffic department head, said he would like the changes to be in force as early as next year.
He pointed out that the new regulations would only apply to new cars.
Friedrich said that the German auto industry would have a more secure future if it was encouraged to build more environmentally friendly cars.
The UBA issued the first draft of its proposals at the end of last month (January).
The draft attracted fierce criticism from some politicians as well as the auto industry.
Germany's environmental minister Juergen Trittin tried to calm the situation down by saying that the tax relief for diesel vehicles with particle filters is the government's priority.