The Scottish airline says it will not operate the daily service between January and May 2020, although some flights will be available at Easter.
Loganair blamed a post-New Year drop off in bookings for the suspension of the service.
The Manchester service was ONLY launched from City of Derry airport in May.
Just 24 hours earlier, the airline announced a new partnership with Flybe saying it was “fantastic news for City of Derry Airport and the wider North West region”.
The news was trumpeted by Derry City and Strabane District Council.
It said in a press release on Monday: “The new code share partnership means travel from City of Derry Airport to a vast range of UK and European airports is now possible by travelling via Glasgow and Manchester with one single booking.
“Passengers are now able to travel from City of Derry Airport to Glasgow or Manchester with Loganair and connect with Flybe to the East Midlands, Birmingham, Exeter, Southampton, Cornwall Airport Newquay, Cardiff, Isle of Man, Jersey, Düsseldorf, Paris Charles de Gaulle and Amsterdam.
On Tuesday, Manchester was taken off the route from Derry.
Loganair commercial director Kay Ryan: “We apologise for inconvenience to anyone who has already booked travel during this seasonal stop in the service.”
She added: “Our forecasts indicate that bookings will be low over the post-New Year period, so we’ve taken the decision to take a break on the route from January 5 until May 21, with the exception of some flights at Easter.”
The airline said customers who have already booked “are now being contacted and offered a full refund or a transfer to an alternative service to Manchester from either Belfast International or Belfast City”.
The decision to axe the route has angered local people.
One told us: “I had booked flights to Manchester for February and got a call last week to say that the route was cancelled.
“It doesn’t look like there are any flights available from March onwards when you look at their website.”
Another fumed: “I had my flights with Logan air cancelled this week.
“I won’t be using them again.
Earlier this month, councillors at Derry and Strabane District Council – which owns the airport – were told almost £6m is required to ensure City of Derry Airport can continue to operate beyond 31 March 2021.
Councillors have given their approval to request additional money from central government.
Loganair took over the London Stansted route in February, following the collapse of Flybmi, which had operated flights on that route since 2017.
Loganair now operates from City of Derry airport to Southend.
The public service obligation air route, the first of its kind in the North of Ireland, has been in place since 2017.