Essex Police said the two men arrested on suspicion of endangerment of an aircraft are both British nationals.
The men, aged 30 and 41, are currently at a police station where they will be interviewed by detectives.
Essex Police said the plane that was diverted to Stansted Airport will remain at its current location until it is examined by forensic experts.
"At this point in time no suspicious items have been recovered", Superintendent Darrin Tomkins said.
"This incident is being treated as a criminal offence and remains under the direction of Essex Police", he added.