Gatwick said so far in 2024 it had safely handled more than 170,000 flights through Nats, a 4% increase on last year.
An airport spokesperson said the service had been fully available more than 99.6% of the time, operating 24 hours a day.
Gatwick typically had 800 or more flight “movements” a day from a single runway.
The spokesperson added: “We will continue to work closely with the Nats leadership team to provide passengers and airlines with a good service.
“London Gatwick would like to apologise to any passengers who experienced disruption yesterday.”
Mr O’Leary has repeatedly criticised Nats chief executive Martin Rolfe, particularly over the widespread disruption at UK airports during last year’s August Bank Holiday Monday, caused by a Nats technical failure.
“Airlines and passengers deserve better,” Mr O’Leary said. “If he won’t go, then new transport minister, Louise Haigh, should sack him.”