Two students from the U.S. Merchant Marine Academy, pictured above, were allegedly drugged during mandatory training out at sea.

(CNN)A cargo ship was sailing across the Atlantic Ocean when the captain summoned two young US Merchant Marine Academy cadets to his room and gave them each a drink.

Shortly thereafter, the students started feeling like something was wrong.

Unbeknownst to them, their boss had spiked their drinks, according to a previously unreported complaint filed by the US Coast Guard. Once they were incapacitated, the captain raped one cadet and attempted to sexually assault the other, the Coast Guard alleges.

The complaint, whichh was filed in August and obtained by CNN through a records request, contends that Captain John Merrone’s conduct was egregious enough that his merchant mariner credential should be revoked so that he is no longer able to work at sea.

The Coast Guard Is responsible for investigating reports of misconduct aboard vessels and can seek to discipline mariners and remove the credential they need to work on ships for a number of violations — from drug and alcohol use to assault. But agency records show that attempted actions against mariner’s credentials for sexual misconduct are rare and slow to occur.

Around a decade ago, Captain John Merrone was accused of rape and sentenced to prison for battery and false imprisonment. His conviction was later overturned in appeals court.

Around a decade ago, Captain John Merrone was accused of rape and sentenced to prison for battery and false imprisonment. His conviction was later overturned in appeals court.

The Coast Guard said in a statement that it initiated its recent investigation as soon as it learned of the cadets’ allegations in 2021. It said the agency’s criminal investigations arm also conducted two separate probes, but that they are not being pursued for prosecution by the Department of Justice and are closed. The DOJ did not comment.

Merrone and his attorney did not respond to CNN’s requests for comment. He denied the allegations in a filing with the Coast Guard.

Merrone’s case comes at a time when the US Merchant Marine Academy and the maritime industry are already facing intense scrutiny of the rampant sexual harassment and abuse that students say they have faced while working and training at sea.

Last year, a student from the academy published an explosive blog post saying she was raped by her supervisor during the school’s mandatory Sea Year training program.

Those allegations prompted outrage in the maritime industry, leading to new reforms and emboldening other alleged victims of sexual assault at sea to speak up. Another student came forward in June, saying she was repeatedly harassed and groped by older, male crew members and was so terrified of being sexually assaulted that she slept in a locked bathroom, clutching a knife for protection. Amid the controversy, a CNN investigation earlier this year found that policies at the federal academy have created significant barriers to the reporting and investigation of alleged assaults, and that a culture of fear has prevented victims from seeking accountability.

While the Coast Guard’s complaint did not name the academy that Merrone’s two alleged victims attended, the agency told CNN they were students at the US Merchant Marine Academy.

Culture of fear at Merchant Marine Academy silences students who say they were sexually harassed and assaulted

Maritime Administrator Ann Phillips said in a statement that a culture change is “urgently needed,” and that the agency has been continuing to strengthen protections for students. The agency pointed to new safety standards that shipping companies must meet in order to carry academy students during its training program.

CNN is not including the company’s name, the date of the incident, or other specific details from the complaint that may inadvertently identify the alleged victims.

This is not the first time Merrone has been accused of rape. Back in 2011, a woman arrived at a hospital bruised and beaten, saying he raped her in his apartment in the Florida Keys, according to criminal court records that included testimony from the nurse who examined her. Merrone was promptly arrested and sentenced by a jury to two years in prison for false imprisonment and battery, but his conviction was later overturned in appeals court. The Coast Guard told CNN it was unaware of the conviction until it had already been overturned two years later, so no action was taken against his credential.

For now, Merrone continues to hold his Merchant Mariner credential while the case proceeds. That leaves him free to sail — as he has been since the alleged incident occurred.

An executive at the shipping company that employed Merrone told CNN he left in 2021 and said his departure was unrelated to the allegations being made. The official said the company had not received any allegations of sexual assault or harassment against Merrone while he was an employee and that while it had cooperated with a U.S. Coast Guard investigation, the company had never been given any details that the matter concerned an alleged sexual assault. The company said CNN was the first to provide details of Merrone’s alleged misconduct and that it would work closely with the appropriate authorities and had launched an internal investigation into the “disturbing allegations.” (CNN)

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