Glasgow to Stornoway and Aberdeen to Kirkwall flights are to be suspended by Flybe.
The services, operated by Eastern Airways, were run in competition to Loganair but have proved to be uneconomical.
The last services will be operated on March 4.
Flybe said the decision was taken because the routes had not shown signs of being commercially viable, the BBC reported.
The airline also announced it is to add 12 flights a week and a Sunday service between Aberdeen and Stornoway.
Scottish carrier Loganair has agreed to assist by honouring Flybe forward bookings on services between Stornoway and Glasgow.
Flybe’s chief commercial officer Roy Kinnear said it had become evident that the Aberdeen to Kirkwall route was not commercially viable for either Flybe or Eastern Airways.
On the other route, he said: “We are naturally disappointed that passenger volumes on the Glasgow to Stornoway route have remained below the level needed to make it commercially viable for either Flybe or Eastern Airways.
“However, we look forward to Eastern’s established franchise flights continuing to serve customers travelling between Stornoway and Aberdeen.”
Increased frequency on this route would “enhance the opportunities” to connect with Flybe’s flights from Aberdeen, including to Heathrow, Manchester and Birmingham, he added.
Loganair managing director, Jonathan Hinkles, said: “The competition has been short-lived but intense, and we are grateful to the people of the Northern and Western Isles for their tremendous support, which has been unwavering – seeing over seven in every ten passengers choosing to fly with Loganair.
“Our priority now is to continue the focus on providing the reliable, cost-effective and sustainable air services for Scotland’s most remote communities.”