Ryanair insists customers who do not want to pay for a preferred seat are randomly allocated one free of charge.
Scientists at Oxford University were asked to investigate the randomness of the airline's seating arrangements for the BBC consumer affairs programme, 'Watchdog'.
Four groups of four non-seat reserving passengers were sent on four separate Ryanair flights.
On all the flights, every one of the travellers was allocated a middle seat.
The researchers calculated that the likelihood of all four travellers randomly ending up in middle seats on each of the flights was around 1:540,000,000.
In comparison, the odds of winning the UK National Lottery jackpot were 1:45,000,000.
Dr Jennifer Rogers, director of Oxford University's Statistical Consultancy, said: "This is a highly controversial topic and my analysis cast doubt on whether Ryanair's seat allocation can be purely random."
A bookings form advert on Ryanair's website offering standard seat reservations for £2 says: "Can't stand the middle seat? Don't leave it to chance, take your pick from a choice of seats. Get up to 50pc off reserved seats with prices starting at £2."
A statement from Ryanair said: "We haven't changed the random seat allocation policy.
"The reason for more middle seats being allocated is that more and more passengers are taking our reserved seats (from just £2) and these passengers overwhelmingly prefer aisle and window seats which is why people who choose random (free of charge) seats are more likely to be allocated middle seats.
"Some random seat passengers are confused by the appearance of empty seats beside them when they check-in up to four days prior to departure.
"The reason they can't have these window or aisle seats is that these are more likely to be selected by reserved seat passengers, many of whom only check in 24 hours prior to departure.
"Since our current load factor is 95pc, we have to keep these window and aisle seats free to facilitate those customers who are willing to pay (from £2) for them."