No airline operator "is going to deliberately sell a flight that they can't crew or operate," O'Leary hit back, adding that crew shortages also happen at very late notice.
The security skills of army and defence personnel could help ease the pressure, he suggested.
"That would be something useful that this government could do instead of blaming the airports or the airlines, which doesn't solve anything.
"We are going to have pinch points at the UK airports right through to the end of this summer until the kids go back to school in September.
"And I believe that the best way of solving these pinch points … is to deploy military personnel who are security trained and who could relieve the pressure on airport security and if you relieve the pressure in airport security, you get rid of the queues."
O'Leary isn't the first to suggest drafting armed forces. Just a day prior, Liberal Democrats proposed the same thing.
Sarah Olney, the party's transport spokesperson, said conservative ministers needed to "get a grip" on the situation, especially with the impending Jubilee weekend.
"The chaotic scenes at airports up and down the country have been nothing short of a complete disaster," she said. "That's why drafting Britain's best and brightest logistics minds from the army to get things moving again is a no-brainer."
However, the Department for Transport said they have no plans to use army personnel in this circumstance.
"It is for operators to ensure airports and airlines are appropriately staffed."