[19] The project was initially slated to be completed by 2012, but protests by local villagers, demanding proper rehabilitation and compensation, had resulted in suspension of work in January 2014.

[20] The AAI intervened and held discussions with agitating villagers and paid part compensation allowing work to resume in October 2014.

[27] On 5 December 2019, 35 families affected by the airport's construction signed off on a joint agreement and accepted the first installment in compensation for their loss of land bringing years of protest to a close.

A terminal building measuring 2,380 m2 (25,600 sq ft) with a capacity of 100 passengers, a car park for 80 vehicles and a fire station cum Air Traffic Control Tower was constructed by Ms PABSCON.

These state-of-the-art geogrid soil reinforcement and slope stabilisation techniques were employed as traditional retaining structures and embankments were ruled out as being unfeasible.

Italian geotechnical company Maccaferri given consultancy services to execute the project that envisaged a 150 m (490 ft) wide, 2 km (1.2 mi) long corridor on which the runway and airport buildings were to be constructed.

In December 2018, 21 of SpiceJet's 31 daily flights (nearly 70% of its schedule) were forced to divert to Bagdogra (up to a five-hour drive away) because Pakyong "lacked the requisite navigation equipment for low-visibility situations", being a Visual flight rule (VFR) Airport as originally planned as per MOU 2002 & MOU 2015 among Civil Aviation GOI, Tourism Deptt Govt of Sikkim and AAI.

[30] Airline officials also cited the approaching monsoon season's aggravating effect on flight operations when announcing the service suspension.

[31][32] In addition to fluctuating weather, adequate basic strip area (western side) issues have also hampered commercial flight operations.

Contractors have been "unable to take up Civil works to extend the stretch of basic strip and erect a strong RCC Retaining wall with anchoring system" because the State Government of Sikkim at the time had not compensated few of the affected landowners.

[34] On 18 November 2020, a trial landing was conducted at the airport by SpiceJet involving a Required navigation performance (RNP) procedure and commercial flight operations resumed on 23 January 2021 after a suspension of 19 months.