The plane went down in a farming field in Muan, about 390 kilometres south of Seoul, according to Ji Man Seok, an official at the Ministry of Public Safety and Security.
Ji said the cause of the incident wasn't immediately known but that the plane was believed to have been on a training flight.
Three men were aboard the four-seat plane before it crashed less than an hour after it took from Muan airport.
The dead are a 32-year-old flight instructor and two trainees, both aged 31, according to local fire officers.