Early last year, the Federal Bureau of Investigation sent a secret letter to a phone company demanding that it turn over customer records for an investigation. The phone company then did something almost unheard of: It fought the letter in court.

The U.S. Department of Justice fired back with a serious accusation. It filed a civil complaint claiming that the company, by not handing over its files, was interfering "with the United States' sovereign interests" in national security.

The legal clash represents a rare and significant test of an investigative tool strengthened by the USA Patriot Act, the counterterrorism law enacted after the attacks of Sept. 11, 2001.

The case is shrouded in secrecy. The person at the company who received the government's request—known as a "national security letter," or NSL—is legally barred from acknowledging the case, or even the letter's existence, to almost anyone but company lawyers.

"This is the most important national-security-letter case" in years, said Stephen Vladeck, a professor and expert on terrorism law at the American University Washington College of Law. "It raises a question Congress has been trying to answer: How do you protect the First Amendment rights of an NSL recipient at the same time as you protect the government's interest in secrecy?"