The 34-year-old worker was moving a loaded lift trolley when he fell into the shaft and sustained severe injuries in May 2016.
Exeter Magistrates' Court was told that though the exact cause of the incident could not be established, an investigation by the Health and Safety Executive (HSE) found that the lift doors had a fault which meant they defaulted to locked.
Despite this, the lift remained in use leaving the safety features redundant, according to HSE inspector Emma O’Hara.
Flybe pleaded guilty to breaching s 2(1) of the Health and Safety at Work Act. The company, which has a turnover of £642 m, was fined £100,000 and ordered to pay £9,963 in costs.
Judge Jo Matson said the starting point for a fine was £300,000 and in normal circumstances would consider raising it due to the large size of the company, however she took into consideration the guilty plea, the fact the company has an
exemplary health and safety record and co-operated fully with the HSE investigation.
HSE inspector Emma O’Hara said: 'Despite a fault, busy workers who were moving parts and tools felt compelled to keep the lift in use. The safety features of the lift were therefore made redundant.
'The lift should have been taken out of service or an alternative system of work should have been in place, and this should have been communicated."
The UK government recently helped the company plug a multi-million pound hole in its finances by giving the airline extra time to pay about £100m of outstanding Air Passenger Duty (APD).