The international body is only the latest in a growing number of groups challenging the program, called the Automated Targeting System, since the department disclosed details last month that it screens travelers entering the country. The European Union is also seeking assurances the department is complying with previous agreements -- called undertakings -- when using the program to screen European citizens.
After years of delicate negotiations, the European Union agreed in October to give Homeland Security so-called Passenger Name Record data on European citizens flying to the United States. A PNR is a file of information that airlines create for every traveler, such as payment methods and meal preferences.
The U.S.-E.U. agreement included strong privacy protections that the European Union is now concerned may be jeopardized.
"The information published by the DHS reveals significant differences between the way in which PNR data are handled within the Automated Targeting System on the one hand and the stricter regime for European PNR data according to the undertakings given by the DHS," European Commission Vice President Franco Frattini said in a statement Wednesday.
The European Commission is the executive arm of the European Union. "The Council presidency and Commission have sent today a letter to the U.S. government to request formal confirmation that the way E.U. PNR data [is] handled in the ATS is the one described in the undertakings," Frattini said.
Telmo Baltazar, European Commission counselor for justice and home affairs, said the U.S.-E.U. agreement states that PNR data should be deleted within four years. But Homeland Security said the Automated Targeting System can keep information on people for up to 40 years.
Baltazar indicated that Homeland Security's explanation of the Automated Targeting System could affect negotiations to renew the U.S.-E.U. agreement, which expires in July. "Everything in life affects everything," he said. "We are simply asking for clarity and confirmation ... Doubts have a tendency of creating more problems."
A Homeland Security spokesman said the department is "confident that we handle E.U. data in accord with our PNR agreement and undertakings."
He added: "The E.U. was also confident in our procedures, following a detailed review in conjunction with the E.U. last year. There have been several inaccurate media reports on the Automated Targeting System, so we understand why the E.U. would want clarification."
The spokesman pointed to a review done in 2005 by the department's privacy office on how European PNR data was being used and protected. According to that review, the department achieved full compliance with the representations in the undertakings and has put in place an extensive privacy program that includes employee training and procedural and technical controls.
The privacy office also had no reports of deliberate misuse of PNR information.