NEW YORK – The battle over laptop searches and seizures at U.S. border stations may have come to a head with the filing of a lawsuit against the Department of Homeland Security.The American Civil Liberties Union filed the suit in a New York District Court on Wednesday, citing constitutional problems with the DHS’ insistence that laptops and personal digital assistants are no different than briefcases and suitcases and therefore may be searched at will. The ACLU seeks an accounting of all documents taken from digital equipment by Customs and Border Protection agents, a waiver of fees associated with copying the documents and compensation for the ACLU’s court costs and attorney fees.

“The ACLU believes that suspicionless searches of laptops violate the First and Fourth Amendments,” the lawsuit states.

The disagreement stems from formal guidelines, effective July 2008, that gave CBP agents permission to search laptops at the border. Court cases brought since then have resulted in findings for the government: Most courts have ruled citizens have a diminished expectation of privacy when re-entering the U.S., especially in light of the country’s need to protect itself. Under the guidelines, about 1,000 laptop searches were conducted between Oct. 1, 2008, and Aug. 11, 2009, according to CBP records. Forty-six of the searches were in-depth examinations, the records indicate.

The ACLU has been critical of the policy from the get-go, claiming laptop searches are a heinous violation of privacy, since laptops and other digital devices often contain more personal information than people carry in either briefcases or suitcases. There is nothing in the guidelines to stop CBP agents from copying financial, health and other data and keeping it on file indefinitely, the ACLU has said.

That’s why the civil-liberties watchdog filed a Freedom on Information request in June 2009, attempting to determine exactly what information the CBP had copied and filed. After negotiations between the ACLU and DHS broke down recently, the ACLU felt it had no choice but to file the lawsuit.

“DHS and its components have wrongfully withheld the requested records from the ACLU,” the suit contends.

According to Catherine Crump, a staff attorney with the ACLU’s First Amendment Working Group, “Traveling with a laptop shouldn’t mean the government gets a free pass to rifle through your personal papers. This sort of broad and invasive search is exactly what the Fourth Amendment’s protections against unreasonable searches are designed to prevent.”

Some Democrats in Congress appear to agree. Both Rep. Eliot Engel [D-NY] and Sen. Russ Feingold [D-Wis.] have introduced or plan to re-introduce legislation that would limit border laptop searches.

On Thursday, DHS both unveiled new rules for border searches and defended current policy.

“The new directives announced today strike the balance between respecting the civil liberties and privacy of all travelers while ensuring DHS can take the lawful actions necessary to secure our borders,” DHS Secretary Janet Napolitano said in a statement.

The new rules continue to allow invasive laptop searches without the owner’s permission, but the searches must be done in the presence of the owner unless national security or law enforcement reasons dictate otherwise. The devices or their data may still be held by CBP officers, and data may be still be copied at will without the knowledge or consent of the device’s owner.

However, the new rules caution inspectors at border stations to be especially careful when handling potentially sensitive data like legal or business documents, health information and journalists’ notes.