TUI has cancelled six flights every day from Manchester Airport until the end of June.
It blamed the late cancellations on ‘on-going disruption’ in its operation at the airport.
However, it said flights from other UK airports will operate as normal.
In a statement, the operator said: “We would like to apologise to our customers who have experienced flight delays and cancellations in recent days and understand that many of our customers have been looking forward to their holiday with us for a long time.
“Due to the amount of on-going disruption in our operation at Manchester Airport, we have made the incredibly difficult decision to cancel six flights a day (43 flights a week), from Tuesday 31 May until Thursday 30th June. All other airports in the UK are planned to operate as normal.
“We understand how disappointing this will be for those impacted; however, we believe this is necessary to provide stability and a better customer service at Manchester Airport. We will continue to work closely with all our airport partners and suppliers so we can provide the best possible holiday experience for our customers.
“Customers affected by the flight cancellations will receive a full refund for their holiday, as well as an extra gesture of goodwill. Customers impacted in the next 14 days will also receive information on how to apply for compensation in line with regulations.
“We would like to reassure our customers that cancellations of this nature are extremely rare and would like to thank them for their patience and understanding.”
TUI has not published a list of the cancelled flights, which, according to the Telegraph, amount to about a quarter of its services from Manchester.
Travel agents are concerned that they now won’t be paid for the cancelled holidays they booked for clients.
Travel Gossip has asked TUI if agents will have to forgo their commission for holidays which will no longer go ahead, however it has not yet responded.