The Airbus A330 jet was nearly 40 minutes into its journey to New York on Monday when the two pilots on board became aware of the “rostering error”, the airline said.
Flight VS3 had reached the skies above Ireland before returning to Heathrow, touching down more than one-and-a-half hours after it took off.
A replacement for the first officer was found, and the plane departed again for New York.
Virgin Atlantic insists safety was not compromised.
Virgin Atlantic plane
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Heathrow Airport
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The initial first officer joined the carrier in 2017.
He was fully qualified under UK aviation regulations but had not completed a final assessment flight which is part of the airline’s internal requirements.
Flight VS3 turned back as the captain had not been designated as a trainer.
Control of an aircraft is usually shared between a first officer and the captain, but the latter holds ultimate responsibility for what happens on a flight.
A Virgin Atlantic spokeswoman said: “Due to a rostering error, flight VS3 from London Heathrow to New York-JFK returned to Heathrow on Monday 2nd May shortly after take-off.
“The qualified first officer, who was flying alongside an experienced captain, was replaced with a new pilot to ensure full compliance with Virgin Atlantic’s training protocols, which exceed industry standards.
“We apologise for any inconvenience caused to our customers, who arrived two hours and 40 minutes later than scheduled as a result of the crew change.”
A spokesman for the Civil Aviation Authority said: “Virgin Atlantic has made us aware of the incident. Both pilots were suitably licensed and qualified to undertake the flight.”