Passengers flying to Exeter, Bristol, Liverpool, East Midlands and Manchester will be impacted by what Aurigny is calling a 'firebreak' plan.
The airline says it can not run its full schedule as it is operating with a reduced fleet - partially because a leased plane overshot the runway last month - and it is struggling to lease immediate cover.
Passengers travelling between 1 June and 4 July to the airports listed will be contacted by the airline via email.
Customers will be able to either accept the changes free of charge or request a refund.
The airline says 'lifeline' London routes will face minimal disruption and all summer European destinations remain unaffected.
Aurigny CEO Nico Bezuidenhout says merging the routes is necessary.
"We are looking to consolidate some of our flying to fit with our available aircraft capacity - with routes that are nearby to each other.
Liverpool passengers will be accommodated on Manchester, Exeter passengers onto Bristol, and some level of consolidation between East Midlands and Birmingham.
I'd like to sincerely apologise to our passengers that have been affected by Aurigny's unreliability over the last number of month.
Every Aurigny employee is acutely aware of the impact of disrupted travel plans.
The challenges we face are not due to the launch of new routes or any conflict between profitability and reliability, but stem from unforeseeable events that have unexpectedly reduced our capacity."
Aurigny hopes to have a fully serviceable fleet by 4 July.
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