The agency said that an estimated 97,000 people, not yet included in the official figures, entered the EU through Croatia in the second half of September after Hungary sealed its border with Serbia.
A total of 282,000 migrants entered the EU in all of last year. By comparison, 170,000 entered in September and 190,000 in August this year.
The Greek islands, especially Lesbos, continued to face a massive migratory pressure, with the number of detections in the January-September period reaching 350,000, Frontex said.
Due to an increasing shortage of boats in Libya and worsening weather conditions, the number of migrants arriving in Italy halved in September to 12,000. This brought the figure for the first nine months of the year to nearly 129,000.
The massive numbers of migrants coming to the Greek islands continue to have a direct knock-on effect on the Western Balkan route, where Hungary reported more than 204,000 detections at its borders - 13 times higher than in the same period of 2014, the agency said.