The airline was established and started operations on 26 September 1994. In March 2006, Estonia's Civil Aviation Administration cancelled the Enimex licence for passenger flights. Enimex's Antonov An-72 aircraft had been used for scheduled passenger flights in Finland, but were regarded by the authorities as not intended for passengers. The passenger licence had apparently been granted by Estonian authorities "by mistake", but it had not been cancelled before, because the planes had not been used for scheduled passenger flights. As a result Soder Airlines had to cancel its flights to Finnish Lapland because the plane operated by Enimex was also denied permission to carry passengers by the Finnish Civil Aviation Authority.
23 November 2001 − ELK Airways flight 1007 operated by Enimex the Antonov AN-28ES-NOV on the attempt to land on Kärdla Airport in bad weather crashed into trees about 1.5 km from the Airport. Of the 14 passengers and 3 crew on board, 2 passengers were killed. The investigation determined that the cause of the accident was pilot error.
10 February 2003 − Antonov AN-28ES-NOY on a regular cargo flight from Tallinn to Helsinki, crashed shortly after takeoff from Tallinn's Lennart Meri Airport. The aircraft came to rest about 300 meters from the runway. Two of the three crew members on board were killed.