"The aircraft, which was flying from Colombo to Heathrow, landed safely with Essex Police in attendance," the airport spokesman said.
A spokesman for Essex Police added: "Police officers boarded the aircraft and arrested two men on suspicion of endangering an aircraft."
"The passengers have been removed safely. Enquiries are ongoing."
The nationality of the arrested men was not immediately disclosed.
The remaining passengers are being looked after at a reception centre at Stansted and are due to be transferred to Heathrow later on Saturday.
Stansted remains open and operating normally, the airport spokesman said.