"Sources tell us there are between 500,000 and one million migrants ready to leave Libya," Frontex chief Fabrice Leggeri said in an interview with Italy's Ansa news agency that was published on Friday.
"In 2015 we must be prepared to face a much more difficult situation than last year," he was quoted as saying.
Nearly triple the number of migrants entered the European Union in 2014 compared to the previous year, mainly due to refugees fleeing war in Syria.
An increasingly violent and chaotic situation in Libya, a key jumping off point for migrants, has also helped prompt the huge hike in the number of asylum seekers trying to reach Europe.
Leggeri warned that his organization simply did not have the resources required to cope with the surging numbers.
"If Frontex is expected to carry out more operations we need more resources and staff, and the commitment from member states to make their means available," he told Ansa.
In any case, the border agency – which relies on EU member states to provide equipment such as coast guard boats – "is not sufficient by itself to tackle this enormous problem," he added.
Hundreds of people have died in recent months as waves of migrants from North Africa and Middle East conflict zones try to reach Europe, fuelling criticism of rescue efforts.
The UN refugee agency last month slammed as "woefully inadequate" Triton, the Frontex-run maritime border patrol which, since November, has replaced Mare Nostrum, a much bigger search and rescue operation that was run by the Italian navy.
Over 900 migrants were rescued in the Channel of Sicily this week but 50 others were feared drowned after a boat capsized off Sicily, according to the International Organisation for Migration (IOM).
The organization warned on Friday that the "human smuggling season" was picking up, with nearly 9,000 arrivals by sea this year so far, despite poor weather conditions.
Asked whether he thought the Isis group was behind the rise in trafficking, Leggeri said "we have to be aware of the risks."
"At this point I have no proof that they have control of the illegal immigration situation. But we must be careful," he added.