“They said: ‘You go Bosnia, go, go,’” said Mr. Eboh. “I said: ‘Go where? I‘m not from Bosnia.’ But he brought up his gun and said he would shoot me.”

The Croatian Interior Ministry has disputed the accounts of the two men, calling them contradictory and inaccurate. To support its case, the ministry cited news reports saying the Nigerians were abused and expelled on Nov. 17, but the police have said they checked out of their hostel on Nov. 18.

“The police have no record of them exiting the Republic of Croatia legally, nor have the police officers working on combating irregular migration taken any action towards persons with their first and last name,” the Interior Ministry said in an email on Thursday.

But the International Organization for Migration, a United Nations department that gave assistance to the Nigerians in Bosnia, reviewed the men’s documents and confirmed that their Croatian visas were valid until Dec. 3 — meaning they were in the country legally when they were deported. Records provided by the tournament organizers show they both participated in the table tennis competition.

The incident has highlighted the often violent ways with which European governments have sought to avoid a repeat of the European migration crisis in 2015, when more than a million people made it to Europe without a visa.

Most traveled from Turkey to Greece, before heading to northern Europe via Hungary.

But a deal between the European Union and Turkey has persuaded Turkish officials to make it harder to reach Greece. In turn, Greece has placed greater restrictions on those hoping to leave its northern borders.