Ryanair could be legally forced to recognise trade unions.
The low-cost airline has refused to engage with unions up until now, but the recent roster problems, which grounded thousands of flights, have led to many workers turning to union representatives.
Pilots are this week meeting across Europe to devise a co-ordinated response to the situation.
Liz Blackshaw of the International Transport Workers Federation says it could mean changes for Ryanair.
She said: "There are many ways of a company being forced to recognise unions.
"I mean it's going to be their call as to whether this is something they will be forced to do through the courts or whether it's something they will be forced to do through their own employees saying to them 'this is something we want', and ensuring that all the workers in the Ryanair service have acces to independent representation."
This follows a period of controversy after Ryanair was forced to cancel 2,000 flights in September and October due to pilot shortages.
The staff scheduling issue has triggered thousands of flight cancellations around the world.
The budget airline now faces a compensation bill of up to €20m for the "mess" which left passengers stranded.
Mr O'Leary has taken full responsibilty. He said: "This is our mess-up. When we make a mess in Ryanair, we come out with our hands up.
"Clearly there's a large reputational impact, for which again I apologise. We will try to do better in future."
Mr O'Leary insisted the airline is "not short of pilots". However, it is reported that Ryanair is losing staff to rival airline Norwegian Air who are recruiting pilots to operate from its new Dublin base.