Croatian police say about 27,000 migrants have entered the country since the surge started several days ago.
Police said Sunday that they are still expecting many more migrants to arrive from Serbia in the coming days. They say authorities are setting up tents for migrants to find shelter from rain and cold.
Migrants hoping to reach Western Europe started going through Croatia last Wednesday after Hungary pushed them away from its border with Serbia.
Scuffles broke out in the Croatian border town of Tovarnik Sunday when hundreds of people surged toward a train they hoped would take them to Austria. Police tried to hold back the crowd, but were overwhelmed as migrants tried to climb through the windows of the already packed carriages.
Hungary, which closed its border with Serbia on Sept. 15, erected another steel barrier at the Beremend border crossing from Croatia to try to slow the flow of migrants. But they kept coming.
The sense of desperation increased for migrants as days of intense heat gave way to rain.
"Unfortunately, we sleep here on the ground without anything. It was very cold," said Muhammad Dakiri, a Syrian asylum seeker in Tovarnik. "Suddenly the weather has turned to cold and raining. We couldn't sleep well because in an hour or half an hour we wake up because we're feeling cold."
The small country of 4.2 million is struggling to cope, and is demanding that the European Union offer a unified response when it meets later this week.
Hungary's decision to shut its border with Serbia set off a chain reaction in Croatia and Slovenia that has forced people fleeing violence in the Middle East, Asia and Africa to rush from one European border to the next as they desperately try to find a way north.
Thousands more continue to brave the Mediterranean in rickety boats as they try to reach more welcoming countries like Germany and Sweden. The surge of migrants continues to exact casualties.
Two migrant vessels sank in the eastern Mediterranean on Sunday, killing 13 people. Authorities from Greece to Austria and are struggling to respond.