The pilot was due to fly from Newquay to Gatwick on Wednesday morning before he was removed for a breath test.
A police source told the BBC that officers were alerted after a fellow crew member became concerned.
A police spokesman confirmed a 48-year-old man was arrested.
The flight was then cancelled and passengers faced delays of almost five hours.
One passenger, who asked to remain anonymous, said: “We all got on the plane and then there was an announcement. We were told the pilot was unwell.”
A Devon and Cornwall Police spokesman said: “A 48-year-old man from Crediton, Devon, was arrested on suspicion of being over the drink-drive limit.
“He was taken to Newquay Police Station and remains in custody.”
The airline said: “Flybe can confirm that one of its pilots volunteered to help the police with their inquiries at Newquay airport.
“Flybe is not able to comment further while the police investigation is taking place.”
A Civil Aviation Authority spokesman said: “For pilots the blood/alcohol limit is 20 milligrammes of alcohol per 100 millilitres of blood. For context, the UK drink drive limit is 80 miligrammes per 100 mililitres.”
Sourced from Travel Weekly