The airline said it would be scrapping some 400 out of 2,400 European flights scheduled for today as pilots in Ireland, Germany, Belgium, Sweden and the Netherlands walked off the job.
The warning from the federation came as hundreds of flights across Europe are grounded this morning by Ryanair pilot strikes, hitting tens of thousands of passengers.
Ryanair has been rocked by a series of staff strikes in recent months that have forced it to cancel hundreds of flights and sullied its reputation for reliable service. "The strike may go ahead", judge Theo Roell said.
That topped the 300 flights a day it had to cancel last month when cabin crews in Belgium, Portugal and Spain escalated the staff revolt by going on strike for 48 hours.
Ryanair has described the strike action as "regrettable and unjustified", claiming its pilots are paid more than other budget airlines.
Since then, however, it has struggled to reach agreements.
Around 55,000 passengers would be affected by the strikes, said Ryanair, which has offered customers refunds or the option of rerouting their journey.
The company is eyeing profits of around €1.25billion (£1.12billion) this year, and boasts lower costs per passenger than its competitors.
But Ryanair pilots say they earn less than counterparts at other airlines such as Lufthansa.
But a court said yesterday Ryanair pilots in the Netherlands could not be prevented from doing so.
At a Frankfurt press conference on Wednesday, Ryanair's chief marketing officer Kenny Jacobs said the company's German pilots enjoy "excellent working conditions".
He added that Ryanair had already offered a 20% pay increase this year, and that 80% of its pilots in Germany were now on permanent contracts.
"Ryanair is the only multinational in Belgium that doesn't respect the Belgian law and that's not normal", said Didier Lebbe, a representative of union ACV-CSC, whose demands include securing its pilots pay when they are on stand-by.
The unrest is one of the biggest challenges to face long-term chief executive Michael O'Leary, who was once quoted as saying he would rather cut off his hand than recognise unions and on another occasion crossed a picket line of baggage handlers to help load a plane.
It has already threatened to move part of its Dublin fleet to Poland, which could cost 300 jobs, including 100 pilot positions. And it has responded to worker demands with its characteristically pugnacious approach.
"We want to again apologise to customers affected by this unnecessary disruption and we ask the striking unions to continue negotiations instead of calling anymore unjustified strikes".
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