Modern alternatives to bread and water for punishing minor offenses can include denying a sailor shore leave. The U.S.S. Chancellorsville, a guided missile cruiser, visited Hong Kong in November.

The United States Navy has come a long way, from its first wooden frigates to today’s nuclear carriers. But in all that time, one thing remained almost as fixed as the North Star: A skipper’s power to throw troublesome sailors in the brig with nothing to eat but bread and water.

Though it sounds like something from an old pirate movie, the antique penalty is not only still on the Navy’s books, it is still actually imposed, despite a century of abolition efforts.

A sweeping update of the Uniform Code of Military Justice, passed by Congress in 2016, will take effect on Jan. 1, bringing dozens of changes that are intended to make the system fairer and more efficient. Most are the kind of procedural tweaks that concern lawyers, not sailors. But the bread-and-water part will be felt on all decks.

On New Year’s Day, it will finally go by the boards.

Commanders throughout the armed services will still have the authority to punish minor misconduct in various ways without a trial. But the new law deletes the regulation that authorized ship commanders to confine low-ranking sailors on “diminished rations” — bread and water — for up to three days at a time.

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That regulation is no mere neglected relic from a bygone era. As recently as 2017, a destroyer in the Pacific was known as the U.S.S. Bread and Water because of the skipper’s liberal use of the penalty to punish missteps like missing a curfew or drinking under the legal age.

Many in the Navy will be happy to see it go. But some mourn what they see as an expedient and effective tradition of the seas.

“It sounds medieval, and that is sort of the point,” said Capt. Kevin Eyer, who regularly sentenced sailors to bread and water for minor misconduct before he retired in 2009. “Sometimes you just need to scare a kid. We want them to succeed, but you need to give them a kick in the pants.”

Captain Eyer said that when he joined the Navy in 1982, the penalty was common and never frowned upon by the top brass, who traditionally give ship commanders broad authority.

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But just as attitudes about spanking children have shifted, the culture in the Navy has drifted away from corporal penalties like bread and water, and officers increasingly view them as counterproductive.

“It just seems anachronistic and stupid,” said Capt. Scott Tait, who joined the Navy in 1992 and has commanded two destroyers.

“I actually can’t believe it’s still around,” Captain Tait said, adding that he had never imposed the punishment himself, nor had he seen it used. “People used to joke about putting guys on bread and water, but I was well into my career before I realized I was actually allowed to do that.”

When young sailors need a minor course correction, he said, instead of ordering a spell in the brig, he often orders them to write reports on works by authors like Patrick Henry or Ayn Rand.

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“Some people need to think about character and the consequences of their actions,” he said. “But I don’t want it to impact their permanent record, which could hurt their chances of promotion down the line.”

The change was recommended by an independent Defense Department review group. Asked if the Navy supported the move, a spokeswoman said, “Once drafted, the Navy did not oppose the legislation.”

That bread and water survived so long after the days of tall ships and daily grog rations illustrates the unique requirements of military justice. For major crimes, the military has a justice system somewhat like the civilian courts, with judges and juries, lawyers and formal proceedings. But it also empowers commanders, who may be at sea or in battle, to deal swiftly themselves with minor offenses like disobeying an order or shirking duty. In all military branches, this nonjudicial punishment can include docking pay, reducing rank or restricting troops to quarters.

The Navy is perhaps the most tradition-bound of the services when it comes to discipline. It still refers to the ceremony in which punishment is meted out as “captain’s mast,” recalling the days when a guilty sailor would be tied to the ship’s main mast and flogged with a cat-o’-nine-tails until his back was bloody.

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Congress outlawed flogging in 1862, after repeated complaints from sailors that tyrannical captains were wielding the lash unfairly. But ships still had to spend months at sea, far from the police, courts or jails, so commanders insisted on retaining special authority to summarily punish and confine sailors.

In those days, bread and water was seen as a humane, progressive alternative to flogging. Under 19th century Naval regulations, commanders could impose it for up to 30 days at a time, and had the option of adding thick iron shackles. Civilian captains used the practice as well.

A New York Times correspondent described the effects of the punishment in 1887 when a sailor in San Francisco was pulled from the dark hold of the American merchant clipper Undaunted: “Heavy irons encircled both his ankles and wrists. His cheeks were hollow, his eyes sunken, his lips were bloodless, and his entire countenance bore signs of great suffering.” The sailor said his only offense was to have refused a promotion.

Sailors soon complained that commanders could be just as tyrannical with bread and water — or as crews wryly call it, “cake and wine” — as they had been with flogging, and there were repeated attempts to end the practice. One secretary of the Navy called for abandoning it in 1882, saying it “meets with the disapprobation of the department;” another tried in 1921 to get Congress to abolish it, saying that using it to try to instill discipline and order “has the opposite effect, and less and less have wise officers resorted to it.”

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The punishment was originally modeled on a British naval practice. But the Royal Navy stopped using it in 1891, a spokesman said, adding, “In my experience, we have always fed our people.”

Though ship commanders in the United States managed to keep bread and water on the books, criticism steadily whittled away its severity. New regulations in 1909 limited sentences to seven days instead of 30, and sailors could no longer be clapped in irons. In 1951 the limit came down to three days. By the 1980s, a medical examination was required before the sentence was imposed.

Today, the rules say sailors are entitled to three unlimited servings of bread each day. Sailors also can typically have their choice of religious books to read in the brig.

“It’s not that bad — that’s why I like it,” Captain Eyer said. “It sounds scary, but it’s just three days, you get as much bread and water as you want — a captain can do much worse things.”

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Punishments that captains will still be able to impose include extra duty for up to 45 days, restriction to the ship for up to 60 days, loss of rank, and half-pay for two months.

“If you are married, every punishment I give you is also a punishment for your family,” Captain Eyer said. “I take your pay, I take away your family’s pay. I don’t like to do that. With cake and wine, the main impact is to the person causing problems.”

But Captain Tait said that even under modern rules, bread and water can still be needlessly harsh.

“Being at sea, there is a lot of sensory deprivation,” he said. “Everything is the same, every day. Meals are one of the few things that actually change. To take that away from someone is more meaningful than people would think.”

In online forums where sailors sound off about Navy life, the views posted on bread and water are mixed. Some said three days in the brig was better than losing pay or being stuck onboard when a ship made a port call. Others saw the punishment as demoralizing and the mark of a poor leader.

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Legal experts say bread and water’s demise will not free the military justice system of all its troublesome relics. Eugene Fidell, who teaches military law at Yale Law School, pointed to how authority over legal proceedings remains in the hands of commanders, rather than an independent judiciary.

“That’s the real archaic part of this,” Mr. Fidell said. “We adopted that practice from the British centuries ago. The British gave it up a long time ago, but we never did. We’re more British than the British now.”

Correction: Dec. 25, 2018 A photo caption for an earlier version of this article incorrectly identified the U.S.S. Chancellorsville. It is a guided missile cruiser, not a destroyer. Dec. 25, 2018

Correction: Dec. 26, 2018 An earlier version of this article referred incorrectly to the Supreme Court review process for disciplinary cases. Reviews to the Supreme Court are handled by the United States Court of Appeals for the Armed Forces, not by the military itself. Dec. 26, 2018

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