"This was the lowest number of illegal border crossings since 2013," Warsaw-based Frontex said in a statement.
The agency said the decrease was largely due to Covid-related restrictions on movement in 2020.
But, while overall numbers were down, Frontex said there was an increase through the West Africa, Central Mediterranean and Western Balkans routes.
It found the migrants detected were most often Syrians, followed by Tunisians, Algerians and Moroccans.
The biggest decrease was seen along the Eastern Mediterranean migratory route through Greece, where numbers fell by more than 75 percent to around 20,000.
The number of illegal border crossings in the Western Mediterranean decreased by 29 percent to 17,000.
But the Canary Islands saw a record number of arrivals in 2020. In total more than 22,600 illegal border crossings were detected on this route -- eight times more than the tally in the previous year.
"Smugglers often used large fishing vessels capable of carrying a larger number of people that departed from West African countries such as Mauritania, Senegal and the Gambia," the statement said.
The number of illegal arrivals in the Central Mediterranean also almost tripled to over 35,600, making it the most active migratory route into Europe.
The number of irregular migrants on the Western Balkan route also rose by over 75 percent to around 27,000.
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