"One of the main pillars in the grievance, is that numerous Ryanair pilots do not have a fixed permanent contract", he told Newsnight.
The bill for the compensation for passengers left stranded and forced to re-book could reach €20million.
Ryanair's chief executive Michael O'Leary said that people whose flights are canceled will be transferred either to another flight on the same day or to a new schedule a day before or after their original date of departure.
In a letter seen by the BBC, pilot representatives from 30 of the company's European bases said most want new contracts and better working conditions instead.
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Several Ryanair pilots have contacted The Independent with their accounts of the causes and consequences of the issue in recent days, with one saying that online groups are forming and "unifying to get Ryanair to make improvements". Norwegian, a rival low-priced carrier with outsized ambitions, claims to have recruited over 140 Ryanair pilots this year (out of around 4,200 at the Irish carrier).
If Ryanair is found to have violated consumer rights, it could face a significant fine.
He also said that Ryanair does not require the agreement of the pilots to take back the leave, and said that all the cancellations would likely cost the airline about €25m (£22m).
The airline has hired additional customer service personnel to accelerate the handling of flight change requests and the reimbursement of the passengers concerned.
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Loizos Heracleous, a professor of strategy and organization at Warwick Business School, said it is surprising that a company so focused on optimizing operations "could be caught out like this", and that it is mushrooming into a much bigger problem.
Ryanair said Thursday it expects to have re-accommodated or refunded more than 95 percent of customers by the end of this week.
They are said to be looking for permanent local contracts for all employees.
"There's an underlying problem at Ryanair, which is quite simply that the company can not replace pilots as fast as they quit", he wrote.
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He told Today with Sean O'Rourke that Michael O'Leary's claim that discontent among pilots is fuelled by unions, is 'absolutely incorrect'.