Transport minister Derek Mackay is to "push" Loganair on its engineering commitments to improve the reliability of its planes.
The minister said the service "has got worse" and the "reliability issues have not been acceptable."
It follows ongoing aircraft breakdowns and flights regularly being delayed or cancelled due to "technical faults."
Mr Mackay was quizzed by MSP David Stewart in the Scottish Parliament.
Mr Stewart pointed out the pilots’ union, Bulpa, expressed concerns that aircraft have been returned to line in poor condition.
Transport minister to "push" Loganair over reliability
11 November 2015
Derek Mackay replied: "I go by what the pilots and the company have told me. We express concern about reliability but we must not put safety in question.
"No Loganair pilot would fly if they thought that the aircraft was unsafe."
He sought assurances from airline officials on 15 September and would seek a progress report on improvements.
Derek Mackay added the Scottish Government has increased the air discount scheme air fares subsidy to 50% and "I expect enhancements around engineering."
He stressed: "Safety must never be compromised."
Last night David Stewart said: “Clearly we are all aware of some very serious incidents involving Loganair.
"Even the transport minister has stated that he is concerned about reliability.
"I am content that the transport minister is going to speak again with officials from Loganair to seek updates on their engineering improvement programme, but my constituents and the passengers that are using these aircraft want real reassurance that safety will not be and has not been compromised and the chief executive of Loganair should come out again and give all users of this service his 100% guarantee that safety will never be compromised and they will take positive action to improve the services provided.”
Loganair has said safety is never compromised and pilots would never take-
The airline is working hard to improve performance including reviewing its operation to improve both punctuality and reliability of services."