Flybe say that they 'sincerely apologise' for the cancellations and say they will issue further updates throughout the day.
Flybe statement in full:
"Flybe sincerely apologises to all our customers and partners affected by the current flight cancellations. Whilst 95% of Flybe flights are operating as per normal, we do recognize the impact of today’s cancellations.
"We are doing our best to mitigate the impact of the current situation that has arisen due to a combination of factors including seasonality, pilots’ end of leave year, Easter holidays, base restructuring and the shortage of pilots across the industry that Flybe has highlighted over recent months.
"We have already identified several mitigation actions and will be issuing further updates throughout the day.
"All those affected have been emailed and advised they can re-book for travel on an alternative flight or apply for a full refund.
"Customers are advised to regularly check our website for more details."
The 7.20am departure from Edinburgh Airport to Southampton was cancelled along with the 1.20pm from Manchester, while the 7am flight to Birmingham was delayed until 8.35am.
Aberdeen International Airport has also been affected, with the 10.40am arrival from Birmingham cancelled, along with the 11.55am from Humberside and the 1.50pm from Belfast.