The U.S. Merchant Marine Academy at Kings Point has navigated troubled waters for years, from leadership turnover to federal funding cuts to concerns over facilities.

But this is likely its most challenging moment — and the seas are high.

The school’s problems must be met with sweeping and substantive reforms to its administration, culture and programs. To successfully steer through it all, federal overseers, and the academy’s leaders, along with students, parents, and alumni, should start by grasping the seriousness of the problems.

The Merchant Marine Academy should be one of the nation’s and the Island’s bright stars, as one of five U.S. service academies. Its graduates work in international waters in commercial trade and in the delivery of military supplies.

But its crisis casts a long shadow over the school’s accomplishments. The Merchant Marine Academy has the highest rate of sexual harassment and assault of any U.S. military academy. Confidential surveys, whose results are reported to Congress, show that more than 60 percent of the school’s female students and 11 percent of male students reported experiencing sexual harassment, while 17 percent of women and 2 percent of men said they had encountered sexual assault.

Also disturbing, most victims don’t report incidents when they occur.

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There’s more. The Merchant Marine Academy also has come under fire from the Middle States Commission on Higher Education, which accredits colleges for the federal government. The commission has given the school a warning, saying the academy failed to meet five of 14 standards. The academy has two years to comply with the recommendations. The commission cited a lack of leadership, along with a failure to properly budget, plan and hire key staff. In a report in June, it pointed to the school’s insufficient response to the sexual harassment and assault reports among the litany of problems.

The academy, which opened in 1943, offers majors in everything from marine engineering to shipyard management. Graduates receive a bachelor of science degree and a merchant marine license. About 2,000 high school students apply each year for more than 250 spots. Applicants submit transcripts and essays, take a fitness assessment and need a nomination from member of Congress.

The school began admitting women in 1974, the first service academy to do so. But only about 15 percent of its 2016 graduating class was female, though that proportion is slightly higher in current classes. The gender disparity, too, is a problem, but won’t be solved until the other troubles are addressed.

As at the other service academies — West Point, Annapolis, the Coast Guard Academy and the Air Force Academy — Merchant Marine midshipmen do not pay tuition. Graduates become merchant marine officers on commercial or federal ships. Postgraduate obligations also can include serving in a U.S. reserve or National Guard unit, or on active duty.

The centerpiece of a Merchant Marine Academy education is its Sea Year, a period during sophomore and junior years. Unlike at the Coast Guard, Navy or similar academies, the school requires students to spend a full year at sea, usually on a commercial vessel.

That is, until now. Officials say a disproportionate amount of sexual harassment and assault takes place during the Sea Year. So, this spring, Transportation Secretary Anthony Foxx put a stop to the program, a decision he then amended so students could be allowed on federal ships, but not commercial ones.

The Sea Year rightly worries federal officials because students are on their own, often without ways to communicate or connect with those on land, and with little oversight. Parents, alumni and students objected to discontinuing Sea Year, worrying that students wouldn’t graduate on time and that the tumult would hurt recruitment and morale. The focus of any change, they said, should be on campus.

But it’s during Sea Year when school and federal officials lack control. So, they’re right to suspend the commercial Sea Year until they understand the problem and find solutions at sea and on land.

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The federal government issued a request for proposals to find experts to conduct a complete evaluation of the academy; the deadline to submit a proposal was Friday.

Whoever wins the contract and the school should make an essential element of the survey an outreach campaign that encourages honesty and openness. It’s the only way to uncover all of the academy’s problems.

The experts should leave nothing untouched. That evaluation should proceed quickly, and once it is completed, the school’s response should be timely and public. The academy’s superintendent, Rear Adm. James Helis, admits there’s no easy fix.

This is a critical turning point. While the Merchant Marine Academy is a local institution, its troubles are a national problem. The school has to do what’s necessary to provide an academically strong and socially safe environment for its students.

It’s time to right the ship.