FOR FAR too long, U.S. officials have operated the no-fly list in secrecy, barring people from planes without offering them an explanation or a meaningful way to get off the list. That may soon end, thanks to a federal court ruling this week in Oregon.

After examining current procedures, security concerns and individual rights, District Judge Anna Brown declared that the no-fly list violates due process. The system contains a “fundamental deficiency,” she wrote, with the result being that “an individual could be doomed to indefinite placement on the NoFly List.” The government currently refuses to alert people to their placement on the list, share evidence that might justify the listing or offer a reasonable way to clear their name. Judge Brown ordered these problems fixed.

The government had argued, implausibly, that the plaintiffs could travel by land or sea. Judge Brown rightly responded that, in the 21st century, the right to international travel is constitutionally protected.

The 13 Muslim American plaintiffs suspect that they are on the no-fly list, but in many cases the government has refused to confirm or deny the fact. A military veteran, Ayman Latif, lost his disability benefits because he could not fly home for his scheduled evaluations. He is now unable to travel on the hajj, the Muslim pilgrimage. Officials detained another veteran, Raymond Earl Knaeble IV, for more than 15 hours when he attempted to return to the United States through Mexico. FBI agents allegedly offered another plaintiff, Nagib Ali Ghaleb, a flight back to the United States if he agreed “to tell them who the ‘bad guys’ were in Yemen and San Francisco and to provide names of people from his mosque and community.”

Mr. Ghaleb’s case illustrates the potential for abuse in such a secretive operation. The no-fly list, created after the Sept. 11, 2001, attacks, is meant to identify those who are a threat to civil aviation or national security. Its purpose was never to become a method of coercion for law enforcement officials. Because of the absence of process, Mr. Ghaleb had nowhere to turn. A case pending in the New York District Court involves plaintiffs similar to Mr. Ghaleb, who were asked to become FBI informants to avoid getting on the list.

This May 11, 2012 file photo, Portland Imam Mohamed Sheikh Abdirahman Kariye, who is one of 15 men who say their rights were violated because they are on the U.S. government's no-fly list. (Rick Bowmer/AP)

In such a complex undertaking, mistakes will happen. Rahinah Ibrahim, dean of a Malaysian architecture school, was put on the no-fly list because an agent accidentally checked the wrong box. She regained her ability to fly only after a lawsuit and a nine-year wait. A transparent process could have remedied Ms. Ibrahim’s problem much sooner.

We sympathize with federal officials who remain under relentless pressure to keep air travel safe. The natural human reaction in such a situation is to err on the side of caution: Better to violate one person’s right to travel, an agent may reckon, than to risk a catastrophe. That’s all the more reason to put in place a system of checks and balances. Rather than appealing Judge Brown’s decision, the U.S. government should accept it as an opportunity for reform.