He admitted "significant management failure" regarding the rostering of pilots, and warned that the moves would not guarantee an end to disruptions.
Italian Transport Minister Graziano Delrio said this week customers' rights had to be protected, adding: "We can not make allowances for anyone who creates so much inconvenience".
The airline has been forced to cancel up to 50 flights daily over the next six weeks - with over 2,000 already scrapped - affecting up to 400,000 holidaymakers.
Ryanair has said it expects up to 20 million euros in compensation claims and 5 million euros in lost fares as a result of the cancellations, though analysts estimated the total cost could be higher.
Instead the pilots made a series of demands including the implementation of permanent local contracts under local employment law, according to the letter, seen by Reuters. "There isn't a union".
Captains at four under-pressure bases have been offered an extra 10,000 euros ($11,914) a year in addition to an offer of a 12,000 euro bonus for those who work an extra 10 days before the end of the year.
Some pilots have rejected Ryanair's offer, which means even more flights may need to be cancelled. The number of passengers affected is less than the initially announced 390,000, because September's preliminary reservations were 90%, compared with 70% in October, the company said.
It's also recruited 125 new pilots to prevent further flights being cancelled.
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.
"I would challenge any pilot to explain how this is a hard job or how it is they are overworked, or how anybody who by law can't fly more than 18 hours a week could possibly be suffering from fatigue", he said. "Ryanair is recruiting new pilots and will probably have to sweeten the deal to reduce pilot turnover, in particular countries where the package is less competitive".
Balpa general secretary Brian Strutton said: "It seems Ryanair has been just about scraping through the summer schedule and having no flexibility in the system, coupled with a miscalculation of pilot annual leave, has led to this disastrous situation".