The barrier at the Hungarian border with Serbia was being used as an illegal crossing point for refugees, but the Hungarian government closed it with razor wire.
It prompted clashes between Hungarian police, who used tear gas and water cannons, and refugees, who threw rocks and attempted to break down border fencing.
Prime Minister Viktor Orban has said he is acting to save Europe's "Christian values" by blocking the main overland route used by many Muslim refugees.
New rules came into effect at midnight Wednesday in Hungary, stating anyone seeking asylum at its southern border with Serbia would be automatically turned away, and refugees trying to break though could face jail.
Mr Orban, speaking to TV2 said: "If someone is a refugee, we will ask them whether they have submitted an asylum request in Serbia.
"If they had not done so, given that Serbia is a safe country, they will be rejected."
Serbia has called the new Hungarian rules "unacceptable" and the United Nations is questioning the definition of Serbia as "safe", saying the state will not be able to house the thousands of refugees that are being turned back.
Viktor Orban says his government by strengthening its borders is simply sticking to EU rules, but critics are accusing his government of being xenophobic.
