Two unidentified men are being held on suspicion of endangerment of an aircraft and they had been removed from the plane, Essex Police said.
Two Royal Air Force (RAF) fighter jets were deployed alongside the Boeing 777 to escort the Pakistan International Airlines flight travelling from Lahore as it was diverted to Stansted, Britain's designated counter-terrorism airport.
"Typhoon aircraft from RAF Coningsby were launched today to investigate an incident involving a civilian aircraft within UK airspace; further details will be provided when known," a Ministry of Defence spokesperson said.
According to Essex Police, the men being held are aged 30 and 41 after its officers mounted the plane at Stansted.
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Passengers said they had heard threats had been made on board, but there has not been any official confirmation of the exact nature of those threats.
A bomb disposal vehicle was seen by the plane. There were 297 passengers on board, besides 11 crew members, who were travelling from Lahore.
The plane was heading west towards Manchester when it was suddenly re-routed near York and headed back out to the North Sea, before travelling south to Stansted.
The pilot, concerned about two disruptive passengers who had started shouting, asked Air Traffic Control to divert to Stansted as a precaution.
Their threats are believed to have been serious enough to call in RAF jets, which are in a constant state of readiness at the Coningsby, Lincolnshire, base in the east of England.
It is understood the incident is not being treated as a terrorist incident and that Essex police are not liaising with counter-terrorism officers at this point.