Travelers seeking to leave on Sunday reported lengthy lines around the terminal as staff raced to manually process luggage.
Stansted said its system, which had recently been through a £70 million upgrade, was likely to have experienced a power outage.
An airport representative apologized for the inconvenience and stated that the issue had been resolved.
Several families who spoke to the BBC at Stansted recounted hectic situations that had put a damper on much-anticipated vacations.
In May, the luggage system was upgraded by replacing worn-out conveyor belts and chutes with 2.4km (7,874ft) of track and 180 automated carts.
According to an airport official, the system was down due to a power failure.
"Contingency measures were immediately put in place with our airlines to mitigate disruption and manually process baggage while engineers worked to fix the issue." The BBC quoted the spokesman
"The system is now operating as normal but passengers are still asked to arrive at the airport at least three hours before their flight departs in accordance with their airline's latest advice."