In May alone, 23,500 irregular migrants made the journey, a rise of 75 per cent on the previous May, it said.
Ukrainians entering the EU via recognised border crossing points were not included in the data.
Five and a half million Ukrainians have reached the EU directly from Ukraine or via Moldava since Russia invaded the country on 24 February, Frontex said.
Some 16,000 -- mostly from Bangladesh, Egypt and Tunisia -- used the Central Mediterranean route
“In the first five months of 2022, the most active migratory routes into the EU were the Western Balkan, Central Mediterranean and Eastern Mediterranean routes,” the agency continued.
More than 40,000 illegal crossings were detected via the Western Balkans -- three times more than last year. Most migrants were Syrians and Afghans.
Some 16,000 -- mostly from Bangladesh, Egypt and Tunisia -- used the Central Mediterranean route.
More than 13,000 crossed via the Eastern Mediterranean, a 116-per cent increase on last year.
Two thirds of those travelled via Cyprus, which saw a 213-per cent rise in crossings.
Most migrants using this route were from the Democratic Republic of Congo, Nigeria and Syria.
On the EU’s eastern land border, the number of irregular migrant crossings rose to 2,155, a more than fourfold increase on the same period last year.
Most irregular migrants using this route were from Belarus, Iraq and Ukraine, Frontex said.
Migrants crossing the Channel in both directions were 122-per cent up on the same period last year, Frontex said.