Ever since President George W. Bush decided to militarize the detention and prosecution of Islamist terrorists, supporters of that decision have claimed that dealing with terrorists as prisoners of war is “tougher” than using F.B.I. agents, Justice Department prosecutors and federal courts.

Charging them in civilian courts, the argument goes, usually with a sneer, amounts to coddling terrorists. And it puts them under the jurisdiction of a court system that is designed to provide due process and protect individual rights. Oh, the horror.

Some of this is political gamesmanship, intended to cow members of Congress into passing laws that steadily erode everyone’s civil liberties, including those of Americans, and to excuse outlaw programs like warrantless wiretapping, indefinite detention, and even the abuse and torture of prisoners. (For former Vice President Dick Cheney, the detention issue also complemented a broader ideological struggle to expand the authority of the presidency at the expense of Congress and the courts.)

Many people, of course, have a sincere belief that the attacks of Sept. 11, 2001, changed everything and that the United States has to consider itself in a perpetual state of war to stay safe.

I think they’re wrong.

As I have argued here, and on the editorial page, the federal courts and prisons are not only the right way legally to deal with most terrorism cases, but also the best way practically. Take a look at an article in the Times over the weekend by Scott Shane, on an aggressive federal prosecution strategy implemented after the Sept. 11 attacks, which has resulted in scores of long sentences, in maximum-security prisons.

Scott reported that there are today 171 prisoners at the Guantanamo Bay prison. Yet there have been only a handful of cases brought against detainees there by a military tribunal system that the Obama administration improved, but which is still deeply flawed and ineffective.

Compare that to the federal system, which is currently holding 362 people convicted in terrorism-related cases, 260 of them with what the federal Bureau of Prisons says is a connection to international terrorism. These people were tried and convicted by the American justice system, not the extra-judicial concoction that has caused untold harm to America’s global reputation.

Sentences are long, imprisonment conditions are tough, and recidivism rates are low. According to the Center on Law and Security, 87 percent of 204 people charged with serious Jihadist crimes since the Sept. 11 attacks were convicted and got an average sentence of 14 years.

So the federal prison system seems to work, efficiently. Guantanamo does not. Which makes it all the more ridiculous that the Senate and the House have passed a bill that would take most of the anti-terrorism effort out of the hands of federal authorities and turn it over to the military. A bill, by the way, that the F.B.I., the intelligence agencies, the Justice Department and the Pentagon believe will hinder anti-terrorism efforts.

I suppose the bill’s defenders would argue that, despite everything Scott’s article lays out, the military system is still better, because the president can hold prisoners at Guantanamo for as long as hostilities continue (meaning forever), without a pesky trial.

But there is a price to pay for the military system, quite literally. According to Scott Shane’s article, a federal maximum-security inmate costs $25,000 a year. At Guantanamo Bay, each detainee costs $800,000 a year.