The glitch has resulted in huge queues of people unable to check in with airlines until the problem is fixed.
Airport bosses say they are investigating the cause of the IT failure.
A Manchester Airport spokesman said: “We are investigating an IT issue that is currently affecting check-in and our teams are working hard to rectify the problem.
“We apologise to passengers for any inconvenience caused and will provide an update as soon as possible”
Passengers say they have been left in long queues with no refreshments.
One passenger, who asked not to be named, said: “Hundreds stuck in terminal one due to check in system failure. Lots of flights affected.
“Hundreds of people just left in queues.”
Another added: “We’ve been waiting to take off for over an hour now. It’s heaving and everyone is fuming.
“There have been no refreshments handed out and no information.”
Other passengers took to social media to voice frustration.