The commission has been condemned for "ignoring" the recommendations of its own experts over safety rules for airline crew, the Parliament.com reports.
The attack came as airline pilots and crew demonstrated over current EU pilot fatigue laws at 22 airports throughout Europe on Monday.
The protest was aimed at raising awareness of the potential dangers of "inadequate legal protection" against the effects of pilot and cabin crew fatigue.
Pilots and cabin crew members handed out fake boarding passes with health warnings alongside detailed information on safety risks.
At a news conference in Brussels, Martin Chalk, president of the European Cockpit Association, pointed out that a report by the European Aviation Safety Agency (EASA) ordered by the commission itself, calls for a reduction in the working hours pilots and cabin crew have to work.
The EASA report recommended that pilots work no more than 13 hours a day without a break and 10 days if working at night.
Current EU rules state that pilots can work up to 14 hours a day without a break and nearly 12 hours at night.
Chalk, head of a group which represents 38,000 pilots, castigated the commission for "ignoring" the "clear and strong" recommendations of the EASA report.
He suggested that the most likely reason for this was the response of the airline industry which had warned of the "damaging" impact of a reduction in pilot working hours.
He said, "Pilot fatigue is considered to be a contributory cause to 15 to 20 per cent of all fatal aircraft accidents.
"It is impossible to be precise, because although the effects of fatigue are as damaging as the effects of alcohol intoxication. There is yet no test to determine the level of fatigue present in a human being in a way there is for alcohol or drugs.
"So this a real problem."
He said the ECA wants EU the transport commissioner to insist that the EASA recommendations are implemented "as a matter of urgency."
"We hope we do not have to organise another day of action."
He compared the EU response to that of regulators in the US where, after the Colgan air crash that killed 50 in February, action was taken to modernise its equivalent set of rules.
"We are determined that we should not have to wait for a similar tragedy on a European airline before our regulator acts," he said.