The plane was bound for Luton but was diverted to Stansted and landed safely.
A spokesperson for Ryanair said: “This flight from Kaunas to London Luton diverted to London Stansted in line with procedures after Lithuanian authorities received a suspected hoax security alert.
“The aircraft landed normally at Stansted and customers will be transferred to Luton by coach when cleared to do so.”
The airline did not give further details of the hoax or confirm initial reports of a suspect package on board.
But there were questions over why the plane was initially allowed to take off after it emerged that the alert was received while it was on the ground in Lithuania.
Local police searched and cleared the aircraft, but a separate alert was allegedly sent to British authorities mid-flight.
One passenger, Jonathan Zulberg, said the flight had been delayed for up to 40 minutes in Lithuania.
“When we were allowed to board we saw fire engines and a police car but weren’t told anything and we took off,” he said.
He said an air steward told him there had been a bomb threat made in Lithuania but other passengers learned that only when the captain made an announcement after the plane had landed in Britain.
“First [the] pilot told us of diversion,” Mr Zulberg added. “Then only once [we] landed after about five to 10 mins the pilot made announcement of a bomb threat.
“When I heard I was pretty surprised the plane was allowed to take off.”
The alert caused jets from the RAF’s Quick Reaction Alert station in Coningsby, Lincolnshire, to be scrambled.
Residents on the planes’ path reported a sonic boom, with many calling Suffolk Police to report “loud bangs”.
An RAF spokesperson said: “The RAF can confirm Quick Reaction Alert Typhoon aircraft were launched this morning from RAF Coningsby to intercept a civilian aircraft.
“The aircraft was safely escorted to Stansted airport. The Typhoon aircraft were authorised to transit at supersonic speed for operational reasons; any inconvenience caused to local residents is regretted.”
Social media users posted pictures of the RAF Typhoon jets following the aircraft through the air and of armed police at the airport.
The incident caused flights to Stansted to be briefly held but the airport was soon operating normally.
Essex Police said the plane landed safely at 8.55am and passengers were taken off and transferred to Luton by bus.
“Officers have carried out enquiries but nothing suspicious has been found,” a spokesperson added.
Chief Inspector Richard Phillibrown said public safety was “paramount”, adding: “We take all intelligence received regarding potential threats to public safety very seriously.”
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