The Ryanair Flight FR2145bound for Luton Airport in Bedfordshire had to be escorted into Stansted airport in Essex instead, with flights temporarily grounded as the plane was redirected.
A Ryanair spokesperson said, "A flight from Kaunas (Lithuania) 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," he said.
Local Essex Police are now investigating the incident.
"The runway was closed for a short time but has now re- opened. Police are on scene and enquiries are ongoing," a spokesperson said.
Britain's RAF aircraft are on stand-by to secure the country's airspace and have the clearance to travel at supersonic speed over land only in emergency situations.
"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," it added.
Stansted is a designated airport for dealing with hijacks and major security alerts in the UK.
An RAF Typhoon jet last escorted a Pakistan International Airlines (PIA) plane to the airport in February.
UK authorities had "received some vague security threat through an anonymous phone call".