Ryanair, a major Boeing customer, has ordered 210 of the more fuel-efficient model and had received 73 by June. O'Leary said a further 51 of the 197-seat aircraft were due by the end of April, including 21 by the end of this year.
"We are concerned that Boeing will not meet those deliveries. They are running late at the moment, there are problems with production in Seattle and we want to understand those problems," O'Leary told a news conference.
"They say they can. We doubt their capacity to deliver. We were supposed to get 21 aircraft this side of Christmas. They are now mumbling it might be 17, it might be 15. It's difficult to get any specifics out of Boeing."
A spokesperson for Boeing did not immediately respond to a request for comment.
O'Leary said Ryanair had agreed during discussions with Boeing last week to go to Seattle to establish when it would be getting the 51 aircraft, which it said were needed to ensure continued growth next year.
The Irish airline flew a record number of passengers for the fourth month in a row in August as it consolidated its position as Europe's largest airline by passenger numbers.
O'Leary said in July that he was confident the aircraft would be delivered but concerned about a possible repeat of delays this year that forced it to take deliveries during its busy summer season.
"At the moment I don't trust what the Boeing team in Seattle are telling us because they keep letting us down," O'Leary told Wednesday's news conference, which was focused on Ryanair plans to stop using Brussels' main airport as a base.
The airline blamed higher airport fees and a Belgian eco-tax.
(Reporting by Philip Blenkinsop; Editing by Padraic Halpin and David Goodman)