The group are among thousands who have fled wars and poverty in Asia and North Africa and are now stuck in Bosnia's northwest region, many without proper shelter as winter looms, and making periodic attempts to pass into the European Union through Croatia.
The violence on Wednesday broke out after around 100 people pushed through a Bosnian police cordon in a march towards the border with Croatia, where they were stopped by another column of anti-riot police from both countries.
Police used batons and pepper spray in a scuffle with those trying to cross the border, leaving three wounded, including one woman who was bleeding from the head.
Two Croatian police officers were also "slightly injured" by migrants who threw stones, Croatia's interior ministry said in a statement.
Croatia's Prime Minister Andrej Plenkovic repeated that his country would continue to "protect its border from illegal entries and migrations".
The migrants, with young children among them, brought tents and appeared ready to spend another night on the roadside near Maljevac border crossing, despite cold weather.
On Wednesday they blocked any traffic from passing.
"We have no other choice, we don't have any money and we cannot stay here, we have no warm place, we don't have showers," Majid Dayyani, a 29-year-old Iranian, told AFP.
Aid groups have repeatedly warned that a humanitarian crisis is looming if better shelter and care is not provided before winter hits.
Bosnian authorities have not set up a formal centre in the northwest region where most migrants are camped out.
Some 20,000 migrants have registered in Bosnia since the start of the year, according to the security ministry.
Many manage to sneak across the border but several thousand are currently languishing in make-shift shelters in the Balkan state.
On Wednesday the government unveiled a shelter close to the capital Sarajevo that can accommodate up to 400 people.
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