Serbia's foreign ministry has protested at Hungary firing tear gas and water cannon into its territory, and says Hungary has now closed the main border crossing for 30 days.
Croatia has opened a route for the migrants - but they face a new risk, from tens of thousands of landmines left over from the Balkans war.
There were chaotic scenes as tensions boiled over at the Serbia-Hungary border.
Desperate to continue their journey to northern Europe, migrants stood in the afternoon heat facing Hungarian riot police, hoping Hungary would open the border.
Some began kicking at the gates - that's when police finally responded.
Tear gas was sprayed into the crowd, panicking men, women and children.
Many stayed to plead and protest until water cannons were used against them.
Some threw rocks and sticks at the Hungarian police.
Hungarian government spokesman Zoltan Kovacs says this is why they must guard their borders.
"These people are not peaceful, they are not simply wanting to go through Hungary. They carry a danger and that danger is very clear and present as of today. " Asked by a reporter if he thought tHese people were not refugees, he responded, "Do you believe that armed refugees would be attacking a police line and trying to come and enter our country? I don't believe so."
The actions of Hungarian authorites have sparked outrage.
Serbian government spokesman Aleksandar Vulin says they violate international law.
"I fully condemn and protest because this is in violation of all international rules. Nobody has the right to throw tear gas in our territory and use water cannons or anything like that."
He says the anger and frustration from migrants is understandable and called on Hungary to open its borders, and allow people to pass through.
UN Secretary General Ban Ki Moon says the dramatic scenes should have never occurred. "I was shocked to see how these refugees and migrants were treated. It's not acceptable."
Serbia is sending more police to its border in an attempt to keep migrants away from the fence and prevent further conflict.
In response to the standoff, neighbouring Croatia has opened up a new route to allow migrants passage to northern Europe.
Croatian authorities are providing buses to migrants, because of landmines in some areas following the war in the Balkans.
The Assistant Director of the Croatian Mine Action Centre, Miljenko VahtariÄ (mil-YEN-ko vah-ter-ITCH), says although the landmines are well-marked, they want to prevent migrants from accidently being caught in the areas.
"There is, according to our estimation, still some 40,000 landmines in the ground. In the whole of Croatia there is 500 square kilometres of suspected hazardous area, and all this area is mark by more than 12,000 warning signs."
Meanwhile the European Parliament has met to discuss the crisis.
This week they'll vote on an emergency scheme to relocate 120,000 asylum seekers from Italy, Greece and Hungary to other member states.
Former prime minister of Belgium, Guy Verhofstadt, says he expects another flow of refugees to Europe if more help is not provided in the Middle East.
He's appealed for more funding to help refugee camps in countries such as Jordan, Lebanon and Turkey where resources and conditions are dwindling.
"My appeal to the European Commission is that they fund immediately, on an urgent basis with the possibilities inside the budget, the United Nations and that they give the money that is necessary in the coming days so that we can in any way improve the conditions of these refugees."
First Vice-President of the European Commission, Frans Timmermans told European leaders protecting borders is part of the solution.
"Please explain to your constituents and to your people back home that our proposals are not just about a distribution key to express solidarity with those states who are really suffering today, they are also about the European Union being able to really better guard its external borders, the European Union being able to offer more support to those states who bear the brunt of this crisis."
The leader the French National Party, Marine Le Pen, agrees.
She says some of the 'open door' policies have had a negative effect.
"You have made Europe a magnet and you have done nothing stop this, and it will submerge us. You assume the responsibilities of your history. This idiocy must stop immediately with a firm and clear policy like in Australia so that the flow is stopped and this chaos stops."
German Foreign Minister Frank-Walter Steinmeier says Germany has decided on its next step in dealing with the migration crisis.
"The German cabinet decided we would participate in the next step of the European Union's Naval Force mission. That means fighting human trafficker gangs. We need to get more information about where the gangs plan the routes they send people on. That's why we agreed to continue our participation in this European mission."
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