Hundreds of irate travellers were hit with hour-long queues stretching back to the check-in desks at the airport on Sunday night.
There had been reports the “unprecedented” problems had been sparked by as many as 13 security staff failing to turn up to work.
But a spokesman today insisted it had been just three security staff who had been unable to work, and said that had added to an “exceptional” volume of passengers.
And he insisted it was now a “priority” to identify the cause of the problem.
An airport spokesman confirmed chief executive Gordon Dewar was “heavily involved” in the probe along with “key members of the management team”.
He stressed that a problem on this scale had “never happened before” and that the airport would be reviewing its procedures. The investigation will examine how visitor numbers are forecast.
The review may recommend that additional staff are put on standby as a contingency measure in case of further staff sickness.
The spokesman said: “We didn’t have enough people to cope with the unprecedented level of people coming through in a relatively short space of time, which did cause some lengthy queues.
“It was an unfortunate incident and we can only apologise. Even if it was frustrating, we were getting people through as quickly and as safely as possible.
“Teams on the ground are working very closely on this as a priority, from executive level right down to floor level to ensure that it doesn’t happen again.”
The airport has not ruled out the possibility that three major sporting events – including the Glasgow derby, the Super Bowl and the final of the Australian Open with Andy Murray – contributed to the unexpected surge of visitors.
Many travellers booked their journeys so as not to coincide with the sporting triple-header, leaving the airport struggling to cope.
But disgruntled regular passenger Murray Lackenby, of Edinburgh, said the new security hall had been a “total shambles” since it opened.
And she added that Monday morning also saw queues “hundreds of people deep in the main hall”.
“It was so bad the escalators had to be switched off as it was dangerously busy on the landing.
“The whole experience was chaotic and aggressive and very badly managed.”
“The new [security] machines are larger and faster, but the staffing has been cut so much the system just can’t cope,” she added.