The area has been accessed by a group of protesters in opposition to the mass deportation of asylum seekers, it is understood.
Despite heightened security following the Westminster terrorist attack, the group managed to gain access to the tarmac and lock themselves together.
Up to eight people are chained together on the runway currently.
End Deportations activist Emma Hughes is one of the protesters at the airport.
She told Huck Magazine: “We’ve taken this action because many people on this flight are being placed in serious danger by being callously deported back to Nigeria and Ghana.
"There’s been a lot of attention recently on Trump’s racist Muslim ban, but what’s happening in the UK is equally repellant."
A Stansted Airport spokesman confirmed flights were running as normal after the delay.
He said: "The protest was to do with a private operator rather than the main terminal facilities.
"The main runway was closed while police dealt with the incident."
