The Eurostat statistics agency said that if the 2016 number was lower than the 1.26 million who came in 2015, it was still more than double the 562,000 of 2014.
Syrians were the biggest single group of first-time asylum seekers last year at 334,800, followed by Afghans on 183,000 and Iraqis 127,000.
Germany, which accepted nearly one million refugees in 2015, took in about 60 percent of the total number of migrants, some 722,300, Eurostat said.
Italy received 121,000 or 10 percent, France 76,000, Greece 49,000, Austria 39,000 and the United Kingdom 38,300.
The fact that the overall 2016 number was only slightly lower than that of 2015 likely reflects delayed recording of asylum requests and the fact that many people do not submit their application immediately on arrival in an EU member state, although under the rules they are supposed to do so.
The main feature of 2016 was the dramatic fall from about one million to around 363,000 migrant arrivals in Greece after an EU-Turkey accord in March that year, according to the International Organization for Migration.
Greece maintains that are still more than 62,000 refugees and migrants stranded in the country, a figure the UN refugee agency called into question Thursday.
A spokesman for UNHCR in Greece estimated the number of migrants at 46,000, saying Greek officials have not taken fully into account the relocation of some refugees while others have been sent back to Turkey or have voluntarily repatriated.
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