Virgin Atlantic's Little Red subsidiary will axe one of its four daily flights between Heathrow and Manchester from the start of the summer 2014 schedule.
The airline began its domestic services in spring 2013 after acquiring nine former Bmi slots at Heathrow from British Airways.
From March 30, Little Red plans to operate Heathrow to Manchester at 09.30, 17.10 and 20.10. Return flights from Manchester will depart at 07.50, 12.20 and 18.50.
The current schedule sees four daily flights depart Heathrow at 09.05, 12.20, 16.45 and 20.05. The return services leave Manchester at 07.25, 10.40, 14.15 and 18.20.
Little Red's domestic network was established to allow Virgin Atlantic to feed regional passengers onto its long-haul network at Heathrow. Flights are operated under contract by Aer Lingus using a single-class A320.
Virgin Atlantic said that the service reduction on Heathrow-Manchester was down to a loss of slots to another carrier, rather than poor demand.
Virgin said the Manchester slots were "loaned from another carrier. We have now had to return these slots to their owner". The carrier in question has not been named.
Slots to Edinburgh and Aberdeen are unaffected because they were awarded to Virgin Atlantic through an agreement made with the European Commission as part of BA’s takeover of Bmi last year.