More than one million applications for asylum in EU member states were under consideration at the end of June 2016, the bloc's statistics agency reported on Thursday.

Eurostat said: "Almost 1.1 million applications for asylum protection in the EU Member States were under consideration by the responsible national authority."

In the same period in 2015, the number was 633,000, the agency added.

The number of people who filed first-time asylum applications in the EU increased by 6 per cent in the second quarter of this year. First-time asylum applications in the 28-country EU reached a total of 305,715 between April and June, up from 287,085 in the first three months of this year, the EU statistics agency Eurostat said.

The numbers came the same day as the head of the EU's executive arm has lashed out at member countries for failing take refugees from overwhelmed Greece and Italy often because the migrants are Muslims.

European Commission President Jean-Claude Juncker said Thursday that some EU states believe that "we are Catholic countries. We don't have any room for Muslims."

Juncker said "I find that kind of reasoning unacceptable. People come first, then religion. It's not religion first, then people."

EU nations voted in September 2015 to share over two years 160,000 refugees in Greece, Italy and any other country unable to cope with migrant arrivals. So far, only around 5,000 refugees have been relocated. At that rate it would take almost two decades to meet the goal.

Europe had struggled last year with a migration surge that brought more than 1 million people to its shores. It managed to disrupt a key sea route from Turkey to Greece in March by negotiating a deal with Ankara, but migrants have also used other routes to reach Europe.

The largest share of applicants continued to come from Syria, making up 30 per cent of the total and with a vast majority of them - 80 per cent - registering in Germany.

Afghans and Iraqis came in second and third place at 16 and 11 per cent of first-time applications. Most of them also sought refuge in Germany.

Six in ten in all applications for asylum were for Germany, the agency said, adding that around 187,000 first applicants registered in Europe's largest economy, followed by Italy (27,000) with nine percent, France (17,800) with six percent and Hungary (14,900) with five percent.

The Syrian civil war has prompted a massive influx of Syrian refugees in Turkey and later to the EU. Turkey hosts around 3 million Syrian refugees.

Compared with the first quarter of this year, applications in Greece - where many migrants remained stuck after the EU-Turkey deal - increased by 132 per cent, Eurostat said. Hungary registered an increase of 118 per cent despite its tough policies against migrants.