The British Airline Pilots Association (Balpa) sent a “strongly-worded” letter to the airline in which it reportedly claimed some planes were “being returned to the line despite being unserviceable”.
It also said that in some cases “aircraft retain defects that clearly affect flight safety”.
However, Balpa stressed no Loganair pilot would fly if they thought an aircraft was unsafe.
The alarm has been soundedfour months after airline chief executive Stewart Adams admitted its flight reliability had “simply not been good enough” and improvements were “critical”.
He announced more engineers would be recruited to fix aircraft faults and the airline had improved its spare parts to cut delays caused by waiting for replacements.
Balpa general secretary Jim McAuslan said: “We’re encouraged by the speed of response by Mr Adams to the letter expressing our concerns.
“This includes arranging meetings to review those concerns, and a tour of Loganair bases to meet pilots and discuss the issues raised.
“Like us, the management are clearly committed to resolving these issues and we will be happy to work with them.
“For the avoidance of doubt, no pilot will fly an aircraft unless he or she believes it to be safe, and in this respect Loganair pilots are no different to those of any other airline.”
Mr Adams said: “The safety of our crews and passengers is and always will be our number one priority.
“The final decision on whether or not a flight departs is always in the hands of the pilot, and we know that none of our pilots would ever leave the ground if he or she had any safety concerns.
“We operate around 34,000 services a year and are subject to regular inspections by the Civil Aviation Authority.
“We hold an European Aviation Safety Agency air operator certificate, and fully comply with all the legislation and safety requirements.
“This demands we must demonstrate we have a fully functional and effective safety management system which specifically manages all aspects of our operational safety.
“We are always open to discussing matters of concern with our flight crews, and have responded quickly to both Balpa and the pilot representatives with an offer to meet
with them at the earliest opportunity to address their issues in detail.”