The EU executive also announced it would help fund a programme of hydrogen research and development called the Fuel Cells and Hydrogen Joint Technology Initiative with 470 million euros (US$664 million) over six years, a sum that would be matched by European industry. It said the programme would "accelerate the development of hydrogen technologies to the point of commercial take-off between 2010 and 2020."
But the Greens party in the European Parliament said the Commission was wasting its time as the technology would not be viable any time soon.
The Commission said hydrogen cars that are ready for the market should be included in the EU's "type approval" system, which determines whether vehicles meet required standards.
The move would simplify approval for hydrogen vehicles and ensure uniform standards were in place throughout the 27-nation bloc, the Commission said.
The proposals require approval from the European Parliament and EU governments before they can enter force.
Industry Commissioner Guenter Verheugen told reporters he did not expect to see many hydrogen cars on European roads in the next ten years, but said petrol-powered vehicles would someday be replaced by models with fewer polluting emissions.
"The car of the future will be different from what we know today. It will not be driven by petrol or diesel," he said.
The Commission is expected to unveil legislation later this year laying out how car companies must reduce emissions of greenhouse gas carbon dioxide (CO2).
The rules will require average CO2 emissions from new cars across the European fleet to come in at 120 grams per km by 2012.
Verheugen said that if the rules were designed to set limits based on an average of individual car makers' fleet emissions, then having clean hydrogen vehicles would be an advantage to producers.
The Greens party was not convinced.
"It is regrettable that the European Commission is still wasting time flogging the dead horse of hydrogen cars when even the car industry itself has abandoned the dream that the technology will be viable in the near future," Claude Turmes, a Greens party member, said in a statement.
"There are clear solutions to the environmental damage caused by vehicle emissions that will deliver real results in the short-term."