Bosnian police had found the migrants near the border late on Tuesday and transferred them to a local hospital overnight, officials said on Wednesday.
The migrants,14 from Pakistan and four from Iraq, alleged they were beaten by Croatian police after crossing into Croatia.
Several men with their hands and arms in casts told Bosnian regional television that the Croatian police had beaten them, taken away their mobile phones and pushed them back to Bosnia.
Evresa Okanovic, director of the local hospital in Velika Kladusa, near the Croatian border, told Al Jazeera Balkans that the migrants had sustained injuries on the hands, shoulders and legs from the beatings, resulting in swelling.
Croatian police said they had prevented 18 men from “illegally” crossing into Croatia on Tuesday night but that according to information gathered so far, the officers had not used force.
“There were no visible injuries on these people nor did any of them ask for medical assistance,” the Croatian police said in a statement, adding that the Interior Ministry will investigate allegations that migrants were injured by police.
Bosnia’s prosecutors have said they are investigating the incident.
“The prosecution … is taking action together with law-enforcing agencies to determine all circumstances of the event,” a prosecution spokesman said.
The Bosnia-Croatia border at Velika Kladusa has become the main gateway for thousands of migrants trying to reach Western Europe since 2016 when EU members Hungary, Slovenia and Croatia began closing their borders.
More than 40,000 migrants and refugees have entered Bosnia since last year.
Human Rights Watch (HRW) said in a December 2018 report that Croatian border officials arrest migrants far inside Croatia, and without due process push them back into Bosnia.
“In some cases, they use force, pummeling people with fists, kicking them, and making people cross freezing streams, and run gauntlets between police officers. Violence is directed against women and children in some cases,” HRW wrote.
In July, Human Rights Watch wrote an open letter to Croatian President Kolinda Grabar-Kitarovic demanding Croatia to stop summarily returning migrants and asylum seekers to Bosnia.
Wednesday’s news follows previous claims from Bosnian officials that Croatian officials were crossing the border illegally in the process.
According to Radio Sarajevo, the Bosnian border patrol had encountered Croatian authorities leading a group of migrants onto Bosnian territory, late on Tuesday.
Once they spotted the Bosnian border guards, the Croatian authorities ran back towards their territory, leaving behind the migrants.
Bosnian authorities complained about the border violations to the Croatian ambassador to Sarajevo in late July and the Bosnian security minister Dragan Mektic last week accused armed Croatian police of crossing the border illegally.
Croatian officials have repeatedly denied the claims.