The European Parliament has voted in favour of referring a draft agreement between the European Commission and the US on air passenger data to the European Court of Justice in Luxembourg.
The European Court of Justice has the power to declare that the yet-to-be ratified agreement contravenes EU law.
The agreement, struck last December, would allow US customs officials to collect 34 different pieces of information about air passengers before they board a plane to the US.
It also would permit US customs to hold onto the information for three and a half years and share it with other government agencies to help them combat terrorism or other serious crimes.
"We regret the European Parliament's decision to refer the agreement to the European Court of Justice," said a US government official in Europe.
"From our perspective the agreement showed the US and the European Union can work together. We stand by the agreement of December."
The draft agreement has yet to be approved by the commission, and according to the commissioner in charge of international relations, Chris Patten, there remain some differences in interpretation of the agreement by both sides.
Patten told the European Parliament that the commission is concerned about the US customs officials passing the data on to other US government agencies, such as the Central Intelligence Agency or the Federal Bureau of Investigation.
"We still need some assurances about this," said Diego de Ojeda, Patten's spokesman, adding that talks with the US Department of Homeland Security are still going on.
"If we are satisfied they have met our concerns we could take a formal decision to approve the agreement. If the US does not do so we may have to take a fresh look at the issue," said de Ojeda.
He said the parliament's decision to go to court is unfortunate. "It is a pity. We hoped the parliament would understand our arguments in favor of signing this agreement."
The European Parliament objected to the agreement throughout the negotiating period. MEPs argued all along that to agree to the US demands would compromise the EU's stricter data protection rules.
Airlines face fines and the loss of their landing slots in the US if they fail to provide the data about their passengers to US customs. Yet if they do hand over the information they may break EU-wide data protection laws.
"We have always said that this agreement represents a bad deal for privacy," said Graham Watson, a liberal democrat member of the European Parliament.
"A big question mark will be left hanging over this agreement until the court rules, so I hope they will be able to do so speedily," he added.
The commission is expected to decide in the coming weeks whether or not to sign the agreement with the US.
Paul Meller writes for IDG News Service