A migrant holds a sack pack on his head as he lies on the railway track in Tovarnik, Croatia September 17, 2015. The European Union's migration chief Dimitris Avromopoulos rebuked Hungary on Thursday for its tough handling of a flood of refugees as asylum seekers thwarted by a new Hungarian border fence and repelled by riot police poured into Croatia. [Photo/Agencies]

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EU commissioner for migration Dimitris Avromopoulos rebuked Hungary over its tough actions, telling a joint news conference with Hungary's foreign and interior ministers that most of those arriving in Europe were Syrians "in need of our help".

"There is no wall you would not climb, no sea you would not cross if you are fleeing violence and terror," he said, describing barriers of the kind Hungary has erected as temporary solutions that only diverted migrants, increasing tensions.

Szijjarto hit back, saying that siding with rioting migrants, who pelted Hungarian police with rocks on Wednesday in clashes that injured 20 police, was encouraging more violence.

"It is bizarre and shocking how some members of international political life and the international press interpreted yesterday's events," he said.

In Brussels, Johannes Hahn, the EU's commissioner in charge of enlargement, urged member states to stay calm and fight the crisis together.

"The Western Balkans must not become a parking lot for refugees. That would be a grave geostrategic mistake. Cool heads on all sides are all needed now, not harsh rhetoric," he said.

Undeterred by the problems faces by migrants at the gates of Europe, more have been arriving at the Greek port of Piraeus from Lesbos island, a short boat ride from Turkey.

Others are waiting outside Europe to attempt the hazardous journey that has cost thousands of refugees their lives.

"It would be very dangerous, but if you make it, the reward is great, the whole world will open up for you," Yousef Hariri, a refugee from Deraa in Syria, said at a refugee camp in Jordan.

Police said the number of refugees arriving in Germany more than doubled on Wednesday to 7,266. The head of the German Office for Migration and Refugees quit for personal reasons after being criticised for slow processing of applications from a record number of asylum seekers.

A record 300,000 people have fled to Europe via Greece this year, according to the International Organisation of Migration. More than 116,000 more have arrived in Italy.

Hungarian Prime Minister Viktor Orban, who has blamed Berlin for the wave of migrants after German Chancellor Angela Merkel rolled out the welcome mat for Syrian refugees, said Muslims would end up outnumbering Christians in Europe if the policy continued.

"I am speaking about culture and the everyday principles of life, such as sexual habits, freedom of expression, equality between men and woman and all those kind of values which I call Christianity," Orban said in an interview published in several European newspapers including The Times.

The UN human rights chief, Zeid Ra'ad al Hussein, denounced "callous, xenophobic and anti-Muslim views that appear to lie at the heart of current Hungarian government policy".