Services from Glasgow to Southampton and Aberdeen to Teesside and Newcastle will end on 10 May along with temporary frequency reductions on seven other routes.
Luke Farajallah has made the changes less than two months after taking over from Jonathan Hinkles following his sudden departure in January.
Loganair said: “The airline has listened carefully to its customers and crew, and under the new leadership team is acting with purpose to address the concerns that have been raised for a considerable time, especially from core markets in remote parts of Scotland.
“The outcome of these changes will see the stabilisation of the daily flying programme, a reduction in the number of flights delayed and cancelled, and less disruption for the Loganair crews and customers who will be able to book and fly with confidence.”
As well as the cancelled routes, several others will see minor adjustments to frequency in varying stages until the end of the summer schedule on 26 October.
Edinburgh to Southampton will be reduced from four to three daily and Newcastle-Southampton from 15 to 13 a week.
Inverness to Manchester will be cut from 11 to nine per week and Inverness to Stornoway from 10 to nine each week.
Isle of Man-Birmingham will have Saturday services removed.
Glasgow to Derry will see Thursday services axed and Glasgow-Donegal will lose its Friday flight.
Farajallah said: “Since my first day as CEO of Loganair last month, I have been listening carefully to feedback from our loyal customers and hardworking crew, and I want to personally apologise to everyone who has been impacted by the unacceptable levels of disruption that have been experienced for over 18 months whilst the airline has been undertaking a re-fleeting programme.
“We appreciate the changes we are announcing today may impact some customers whose bookings may need to change. While we apologise to customers affected, this decision is one that has been made for the greater good of the vast majority of customers who must be able to book and fly with confidence, especially from some of the most remote parts of the UK.”
He added this was “especially true for the Highlands and Islands communities who rely on Loganair for being so much more than an airline serving a leisure market”.
Farajallah said all airlines had experienced aircraft shortages and crew recruitment difficulties “exacerbated by post-Brexit regulations, limiting UK airlines’ ability to recruit pilots from the EU”.
