This generation’s Pearl Harbor, the Sept. 11 terrorist attacks in New York and Washington, aroused Americans much like the Japanese attack 60 years ago that catapulted the United States into World War II. Once again, we were fighting mad. We had been caught napping and feared further attacks. Most of us welcomed extreme security measures. Few questioned Attorney General John Ashcroft’s declaration that “aggressive detention of lawbreakers and material witnesses is vital to preventing, disrupting or delaying new attacks.”

But now that we are fighting back and getting more or less accustomed to living in a new and more dangerous era, sober second thoughts are surfacing. People are seeking the right balance between security precautions and preserving historic constitutional rights. Detain “lawbreakers”? Sure. But what exactly is a lawbreaker in a system that holds any accused person innocent until convicted in a court of law? And what about “material witnesses”?

A federal judge in New York has scolded Mr. Ashcroft and given him a stern history lesson. In a 120-page opinion, she reminded him that the British Crown’s use of “general warrants” to jail colonists was one of the grievances that sparked the American Revolution. She recalled that when the Constitution was first presented to the 13 states for ratification in 1787 it was viewed “as fundamentally flawed because it failed to provide [citizens] protection from the government.” Since Sept. 11, law-enforcement agents have arrested and detained more than 1,200 people, many with no formal charges filed against them. One of them, Osama Awadallah, a 21-year-old Jordanian citizen and permanent U.S. resident, was arrested Sept. 21 as a material witness. The arrest was under a rarely used criminal law allowing prosecutors to detain an individual they have reason to believe has information critical to a “criminal proceeding” if the individual can’t be compelled to testify in any other way. The 9th U.S. Circuit Court of Appeals has upheld such arrests.

U.S. District Judge Shira A. Scheindlin of the Southern District of New York ruled that using the material-witness law “to detain people who are presumed innocent under our Constitution in order to prevent potential crime is … illegitimate.” She held that material witnesses can be jailed only after a grand jury has handed up an indictment, not during its investigation, and only when doing so is the only reasonable way to obtain testimony for trial. She wrote that if a grand jury wants a reluctant witness to testify it should have a subpoena issued.

The case of Osama Awadallah is a complicated one, beyond his unfortunate first name. He was arrested after investigators found his phone number in the car of one of the Sept. 11 hijackers. He was taken, often shackled, from San Diego, where he attended a community college, to New York, held in isolation, unable to communicate with his lawyer or relatives. Judge Scheindlin wrote that he “bore the full weight of a prison system designed to punish convicted criminals” without even an allegation that he had broken any law.

When he was brought before a grand jury, he first said he knew only one of the hijackers by name but later admitted he knew two of them by name. He admitted to meeting with one of the hijackers about 40 times, but the telephone number found in the car was one he had not used for two years. Judge Scheindlin had questioned the government’s case in November, releasing Mr. Awadallah on $500,000 bail over prosecutors’ objections. She called the evidence against him “not particularly strong.” She dismissed the case on April 30, saying that the statements it was based on could not be admitted in court because they came while he was illegally imprisoned as a material witness.

Although the decision involved only the one person, it could lead to filings by many other so-called material witnesses jailed in the aftermath of the terrorist attacks. Mr. Ashcroft is expected to appeal, but the case suggests that the tide is turning. We must protect not only our security against terrorism but also the freedom guaranteed by the Constitution.