MOSCOW — Russia is suspending its participation in a long-running exchange program that has brought tens of thousands of high school students to the United States in protest of one former participant’s decision to stay with a gay couple, Russia’s top children’s advocate said Thursday.

The decision, which comes at a time of increasingly dismal diplomatic relations between Russia and the United States, pokes at open wounds that predate the Ukraine conflict: In 2012, Russia banned U.S. adoptions of Russian orphans following reports of children abused and abandoned by their new families, and since then, Russia has expanded its adoption ban to prevent gay couples from adopting Russian children as well.

“We cannot leave such an egregious case unanswered,” Russia’s Children’s Rights Commissioner Pavel Astakhov said in an interview published by Russian newspaper Rossiyskaya Gazeta Thursday, recalling past instances in which American hosts were alleged to have mistreated visiting Russian children — and stressing that when Russian minors travel abroad, hosts must ensure their safe return. “This is a serious violation,” he concluded.

The FLEX program — or “Future Leaders Exchange” program — has been bringing students from the former Soviet Union to the United States on State Department-funded homestays and fellowships for over two decades. The teenage participants, who face stiff competition for the scholarships — only about 1 in 50 actually secures an award — spend an academic year living and studying in the United States before returning home, which for over a third of program participants is Russia.

But this past May, one of the Russian exchange students did not come home on schedule, Astakhov said during an interview on state television Russia 24 Thursday, and “under the influence” of the gay couple that had taken him in, applied through the Michigan courts to stay on as a refugee. Now, Russian authorities are citing that case as reason to scrap all participation in the long-running program — a decision that left thousands of would-be participants, whose applications were due less than two weeks from now, reeling.

“I felt bitter,” said Lidia Zatolokina, a 16-year-old from Krasnodarsk who had already written two essays — and after making it through introductory rounds of the competition last year, thought her chances of securing a spot this time were good. Studying in the United States is a “unique” experience, she said, that “now, it’s not possible for me to try myself.”

Officials from American Councils, which administers the FLEX program, aren’t disputing the basic circumstances of what happened with the Russian student in question. But they are questioning Russia’s reaction — and challenging officials’ assertions that they were directly responsible.

Though exchange students are occasionally placed with same-sex host parents, David Patton, executive vice president of American Councils, explained, this student had actually been placed in a “traditional” homestay. He did not detail how the student met the same-sex couple to whom Russian authorities are objecting.

“The issue that ensued really was after the program for this individual,” Patton said, adding that less than 1 percent of the tens of thousands of former FLEX students have tried to overstay their terms. “As the implementers, I can say that we lose jurisdiction in that case.”

In Russia, FLEX alumni are also questioning the government’s decision to end the program — and surmising that the reaction may be more political than protective.

“Our government only told us about this four months after it happened, if it really happened,” said David Petrosyan, 21, an alumnus from Rostov who spent his 2009-2010 FLEX fellowship in Kentucky. “I don’t think that anybody can keep a person against his will, or without his parents’ permission. That sounds to me like it’s not as real as they say it is.”

“I was mad, but I wasn’t surprised,” said Anya Laletina, 25, an alumna from the Kirov region who did her 2005-2006 FLEX year in Washington state. She said she feared for the program since American Councils was kicked out of Russia as part of a crackdown on foreign nongovernmental organizations this spring. “Because of the relationship between Russia and the United States, it’s not surprising at all. It’s just another thing in this whole process.”

Russia’s decision will not force students currently in the exchange program to come home early but will take effect in the 2015-2016 academic year. U.S. State Department spokeswoman Jen Psaki said Wednesday that the United States regrets Russia’s decision to cancel its participation in the FLEX program. Over 8,000 Russians have taken part in the program since it started.

FLEX alums hope that the program will be reinstated if Russia-U.S. relations improve. But in the meantime, they say, there is no practical, affordable substitute to send future students such as Zatolokina to the United States for cultural exchange.

“All the magic’s vanished,” Zatolokina wrote on her VKontakte page — where among various links and selfies, she also posts detailed charts of English idioms and proper verb usage. “The Russian story of FLEX may continue, but mine has reached its final destination.”