The IAF aircraft was a fixed wing 19-seater Dornier 228 and it was learnt that all the systems worked well.
The official said that the aircraft made the landing at the airport despite the fact that the visibility was not so clear.
He said several trial low passes were made over the runway on February 28.
''This is the beginning of aviation connectivity for Sikkim,'' the official said.
The Pakyong airport has been constructed at a cost of over Rs 350 crore and is awaiting the nod from the DGCA for beginning commercial operations that will bring Sikkim on aviation map of India.
A private airlines flight is expected to land on March 10 carrying high-ranking officials of the Airport Authority of India and the Directorate General of Civil Aviation, Srivastava added.