If the legislation goes ahead, it could cost retailers an estimated£61 million a year.
The tax would cover carrier bags, bin liners and nappy bags. A vote on the proposal will take place on July 20.
British Retail Consortium (BRC) Brussels director Alisdair Gray said: 'At a time when retailers face energy bills, rents, rates and service charges rising well above inflation, another cost increase is the last thing they need. In the end, whether the bags are paid for or given away, they will have to pass the cost on to the consumer.'
The revelation follows an announcement earlier this week that the EU is proposing to increase the import taxes on leather shoes from the Far East. It plans to run the new levies for at least five years and include children's shoes for the first time.