A Ryanair plane from Lisbon, Portugal unloaded its passengers at a departure gate instead of one set aside for arrivals.
This meant the arriving passengers passed straight into the departure lounge, mixing with people waiting to catch their flights.
Airport procedure meant that everyone in the departure lounge had to leave and go through security again, causing long queues.
London Stansted Airport is an international airport located at Stansted Mountfitchet in Essex, 48 km northeast of Central London.
"Pandemonium at Stansted Airport. Security queue stretches length of terminal twice!," Rob Treloar, a passenger tweeted.
"We are now experiencing queues in the security area with delays of up to an hour on some flights. We apologise for the inconvenience and hope to resolve this matter as soon as possible," ITV quoted a Stansted Airport spokesman as saying.
"We advise passengers travelling to the airport this afternoon to allow a little extra time for their journey," he said.
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