Services from Inverness to Stornoway and Benbecula, and from Inverness to Kirkwall and Sumburgh, will be halted from Friday 17 March to Sunday 30 April.
In December, 73.5% of workers represented by the Unite union at 11 Scottish airports operated by Highlands and Islands Airport Limited (HIAL) voted in favour of outright strike action, and 92.8% in favour of action short of a strike.
The first walkouts were held last month, with Loganair warning ongoing "work-to-rule" industrial action was impacting its ability to operate its schedules confidently.
Loganair said that while definitive strikes could be managed through offering alternative flights or full refunds should passengers choose not to travel, the impact of work-to-rule action was "far less predictable" with the absence of a single member of HIAL staff through sickness or an emergency likely to bring the whole operation to a standstill.
"This leads to a position where shifts cannot be manned to the required minimum levels to enable flights to take place, causing cancellations and delays with either very limited advance notice or none at all," said Loganair.
"Where Loganair flights are operating from HIAL airports to other destinations unaffected by the industrial action – such as Glasgow, Edinburgh or Aberdeen – the impact can generally be managed within operational flexibility available on the day.
"However, where flights are taking place between HIAL airports then the cumulative effect of rolling restrictions at each airport in turn means that it becomes impossible to reasonably assure the provision of a service between them."
Customers booked on affected Loganair flights will be contacted and offered the option of rebooking on alternative routes, or a full refund.
A Loganair spokesperson said: “We completely understand this unprecedented step will be unwelcome news to communities who depend on the air services Loganair provides. It’s a step that we are taking with the utmost reluctance and only after careful consideration of all other options.
"We have sadly concluded that it’s simply not realistic to continue our efforts to provide services between HIAL airports when the action short of a strike is intended to disrupt and counter those efforts at every turn."
The spokesperson added: “The suspension provides advance – even if unwelcome - certainty around which our customers can adjust travel plans, as opposed to facing the risk of on-the-day flight cancellations or significant delays.
"We hope that the period of suspension – initially through to 30 April – will provide time and space for the parties to this dispute to meet and reach a resolution, enabling these long-running services to resume thereafter.”
