Millions of Ryanair passengers booked on flights after 13 June will have shorter check-in periods, in a move likely to encourage more travellers to pay for reserved seating.

The budget airline said its check-in window for passengers who have not paid for reserved seating will shrink from four days to 48 hours. But if customers pay for a reserved seat – which costs from £3 each way but rises to £15 for seats with more leg room – they will be allowed to check in up to 60 days before flying.

The latest rule change at Ryanair comes just months after a controversial change to its baggage policy. Passengers have to pay £5 for priority boarding to avoid having their main cabin bag checked in to the hold at their departure gate. The baggage policy was due to begin in November last year but was delayed until January amid the Ryanair flight cancellations fiasco.

The new check-in policy is likely to encourage weekend-break travellers to pay for reserved seating, or be forced to find ways to check in online while abroad. For many travellers using the Ryanair app on their smartphones, check-in is a relatively simple procedure, but others will find it more daunting.

As recently as 2016, passengers could check in for free up to a week before departure, but this was cut to four days and will now move to 48 hours.

The airline has also faced widespread criticism for running a “pay up or we split you up” seat allocation policy. Couples travelling together who do not pay for reserved seating often find themselves seated at opposite ends of the aircraft, despite Ryanair claims that the allocation policy is random.

Ryanair said the new check-in window brings it into line with rival airlines. In a statement, it said: “Online check-in (for those customers who don’t choose reserved seats) will be available from 48 hours to two hours pre-departure for all flights from Wednesday 13 June. This is double the 24- hour check-in period operated by Aer Lingus, British Airways, Lufthansa, Norwegian and Iberia. This will give reserve seat customers more time to select their preferred seats prior to departure.”

Shares in Ryanair have tumbled since the cancellations issue and prolonged labour disputes. They peaked at €19.35 in August last year, but have since fallen to around €15.72. Meanwhile shares in its main rival, easyJet, which announced upbeat figures on Tuesday, have jumped from around £12 last August to £17.10.