Under the terms of a deal reached after September 11, 2001, European airlines supply the American authorities with information on passengers entering the US including their name, address, payment details and telephone numbers.
An EU court struck down the existing deal on a legal technicality in May but gave the EU and the US until September 30 to replace it.
Negotiators failed to reach a deal on Saturday but both sides said they would try to reach an agreement quickly.
US officials have not said whether they would be willing to apply the safeguards from the lapsed agreement.
Without them, Jonathon Todd, the EU commission spokesman, said there was a risk data protection authorities in EU states would challenge airlines' right to transfer data.
Airlines fear this could leave them open to legal action by passengers.
"There is nothing to prevent the Americans from continuing to apply those safeguards," Todd said. "If they do, there shouldn't be a problem for European airlines that continue to transfer the data."
The Association of European Airlines, which represents carriers such as British Airways, Air France and Lufthansa, has expressed concerns at the possibility of "extreme" disruption to services unless a new agreement is reached.
Spokeswoman Francoise Humbert said that if airlines did not supply data required by the United States, passengers faced having to provide such information at US airports with consequent queues and delays.
A commission statement said a draft agreement sent to the European side by the US homeland security secretary, Michael Chertoff, on Saturday may be discussed by EU justice and home affairs ministers in Luxembourg next Friday, "in the hope of having an agreement the same day".
In the statement, the EU commission urged the US to continue to apply safeguards for passenger data laid down in the lapsed 2004 agreement until a new one was reached in order to minimise the risk of legal uncertainty and disruption to EU-US flights.