The vast majority came via the Mediterranean into Italy and Greece.
The ongoing wave comes despite a deal struck with Turkey in March to close down access to Greek islands, which was hailed as end to the migration crisis.
Tough new controls and returns saw a big drop of 79% in the number arriving in Greece, down to 182 500 – with Syrians, Afghans and Iraqis making up the largest share.
Official figures say around half a million illegal immigrants came into the EU last year
But at the same time, a record 181,000 crossed the central Mediterranean from Africa – a 20% rise from the previous 12 months.
The significant majority on this route were from West African countries, with Nigerians made up the largest portion, followed by nationals from Eritrea, Guinea, Côte d’Ivoire, and Gambia.
The 2016 annual total is less than a third of the massive 1,800,000 estimated to have entered the EU in 2015.