A few houses were damaged, the officials said.
The rain water also damaged drinking water pipelines at Mamzey village below the airport area.
Meanwhile, a senior Airports Authority of India (AAI) official at Pakyong solicited cooperation of the state government and the local officials in helping the AAI acquire land below the airport wall, so that houses lying there do not have to bear the brunt of heavy rains.
"We want the state government to assist us in getting the land of the local people residing below the airport's perimeter," Deputy General Manager (AAI) at Pakyong airport, Jagbir Singh, said.
The Pakyong airport, located at an attitude of 4,500 feet, has been constructed at a cost of Rs 605 crore.
The state of Sikkim, nestled in the Himalayas, is set to join the aviation network of the country, since the Pakyong airport obtained license in the first week of May this year.
Civil Aviation Minister Suresh Prabhu took to Twitter to announce the development, saying the license would pave the way for direct air connectivity to the state, giving a boost to tourism and economic growth.
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