Ryanair will close airport check-in desks 20 minutes earlier to avoid passengers missing flights, it has announced, amid concern over border queues in Europe.

The budget airline, which carries 200 million passengers annually, will require all passengers dropping bags or checking in at the airport to do so one hour before take-off rather than the current 40-minute deadline.

Ryanair said the change, which will take effect from November, would give more time for passengers to clear airport security and passport control and reduce the number who miss flights through being stuck in queues.

While the move was not prompted by the introduction of Europe’s entry-exit system (EES), which requires most non-EU citizens to provide biometric data at the border, the airline said the system had been a factor in increasing passport queues.

Waits of several hours have been reported at some airports in the phased introduction of EES since October. Greece this week said it would not enforce the new checks on UK nationals this summer for fear of summer border chaos. More than 100 passengers missed an easyJet flight this month due to passport queues in Milan after the system officially came into full effect.

Ryanair said most passengers would be unaffected by its check-in change, with about 80% completing the formalities online and going straight to the departure gate. Only about 20% of its customers check in bags at airports, with most paying for cabin bags or travelling without luggage.

The airline said that by October it would have installed self-service, bag-drop kiosks at more than 95% of its airports. Ryanair’s chief marketing officer, Dara Brady, said it would mean a “quicker bag-drop service, less queueing at airport desks, and an even more punctual service for the 20% of our customers who still wish to check in a bag”.

The Irish airline, Europe’s biggest by passenger numbers, has been at the forefront of changes to baggage rules, including making passengers pay for cabin bags. It has been notorious for strictly enforcing sizes, incentivising staff to catch and fine transgressors.

While many of the changes have prompted an initial outcry, the airline’s chief executive, Michael O’Leary, has been unapologetic and suggested the travelling public should be grateful for the encouragement to travel light.