Furious passengers took to social media to share pictures of the mayhem.
Commuters complained they had missed flights because of the delays, despite being told airlines were aware of the issues.
One traveller even described the scene as being like a “zombie apocalypse”.
An airport spokesperson said: “Due to a technical issue this morning with a number of X-ray machines in the main security area, throughout capacity was reduced, taking extra time to process passengers.
“Engineers are rectifying the issue and additional staff and machines are in operation. We are liaising with airline partners to minimise the impact to passengers.
“We apologise for the inconvenience.”
Just after 8am the airport tweeted to say the “IT issue” had been resolved and it was working to assist passengers with their onward travel.
One passenger – named as David – added that a “passenger fainted and wheelchair passengers cannot get through”.
Others criticised the “sheer incompetence” and described the scene as a “shambles”.
Earlier this year, Stansted Airport was closed after a runway was stormed by protestors.