[3] With a start-up capital of 10 million rupiah, Merpati began operations in Kalimantan, using a fleet of four de Havilland Otter/DHC-3s and two Douglas DC-3 Dakotas provided by the Indonesian Air Force (TNI AU).

Pilots and technicians were supplied by the Indonesian Air Force, Garuda Indonesia Airways, and other civil aviation companies.

With the addition of three DC-3 Dakotas, two DHC-6 Twin Otters and 1 DHC-2 Beaver, Merpati began to grow, with operations now reaching Sumatra, Papua and Nusa Tenggara Barat.

Further expansion saw the addition of more aircraft, including three Dornier DO-28s and six Pilatus Porter PC-6s, and staff numbers growing to 583 people.

[5] In February 2014, due to the airline's inability to pay its employees salary or benefits for three consecutive months, many pilots and cabin crew resigned.

[6] The same month, Merpati suspended all services due to cashflow problems, including an inability to obtain fuel on credit, obliging the company to pay cash.

Courses conducted by the MTC include type rating courses for pilots, flight attendants and flight operation officers on the Boeing 737 Classic, AVIC Xian MA60, Fokker F27, CASA CN-235, DHC-6 Twin Otter, CASA C-212 Aviocar, as well as other ground courses including Dangerous Goods Awareness, Airline Transport Pilot License (ATPL) theory, Cockpit Resources Management (CRM), Reduced Vertical Separation Minimum (RVSM), Approach and Landing Accident Reduction (ALAR), Safety Management Systems (SMS), Aviation Security (AVSEC) and Windshear Avoidance.

On 16 February 2010, the Merpati Pilot School, a department of the MTC, was officially launched at Surabaya's Juanda International Airport.

The flying school was awarded its Part 141 certification from the Directorate General of Civil Aviation on 18 August 2009 and currently has a fleet of four Cessna C172s, registered PK-MSA, PK-MSH, PK-MSN and PK-MST.