Bosnian police are stepping up patrols as thousands of migrants have already made the journey into the country via the Serbian border.
From there, they head to the border with Croatia, which is a member of the EU.
Up to 50 migrants were stopped by Bosnian police yesterday after they were found in a cargo train headed for Serbia.
The train stopped on Friday had been carrying coal and was halted near the Bosnian border town of Zvornik on the banks of the River Drina.
As the train was stopped, some of the migrants onboard jumped out and started running with many racing back to Serbia.
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A group remained on the train and were then turned back to Serbia.
Local police gave no further details, but added that asylum seekers that mostly came from Afghanistan, Iran, Syria and Pakistan reach Serbia via Albania and Montenegro.
Bosnia had not been on the well-trodden migrant route through the Balkans to European Union nations until earlier this year when arrivals jumped.
About 11,000 people from Asia and North Africa have been registered as arriving so far this year.
A police source who asked not to be named said: “Migrants are crossing the River Drina (the border between Serbia and Bosnia).
“They pay between €250 to €300 (£225) to smugglers to take them over the Drina.”
A police source said that some go to beaches on the Serbian side pretending to be tourists and then swim to the Bosnian side before walking west to attempt to cross into other EU member state Croatia.
Croatian police have recently upped border controls and have now turned back migrants.
About 5,000 of them remain stranded in Bosnia.
Croatia was the last nation to join the EU and became the bloc’s 28th member in 2013.
Still recovering from a devastating war in the 1990s, Bosnia was bypassed in 2015 and 2016 when more than a million migrants and refugees passed through the Balkans. But as borders have closed elsewhere, Bosnia has become a new transit route.