BRUSSELS—Large numbers of Syrian and Eritrean refugees are stranded in Libya waiting to be illegally smuggled to the European Union, the deputy head of the bloc's border agency warned on Wednesday.

Over 26,000 migrants have arrived in Italy by boat from Libya in the first four months of this year, more than eight times the number of arrivals in the same period last year, said Gil Arias Fernández, the deputy executive director of Frontex, the Warsaw-based EU agency that coordinates border patrols and collects intelligence about...