The vote counting began in 11 local units of Kathmandu and 6 local units of Lalitpur district after an all-party meeting forged consensus at National Assembly Hall.
Ballot boxes from Ward Number 1 were opened first to begin the counting.
Helicopters were used for airlifting ballot boxes from mountainous districts to district headquarters.
According to Election Commission spokesperson Surya Prasad Sharma said helicopters were mobilised in Rasuwa, Dhading, Dolpa, Humla, Gorkha and Mugu districts.
The first phase of local elections was held successfully across three provinces yesterday to choose leadership in Kathmandu Metropolitan City (KMC) and its 32 wards .
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The first phase of the local elections took place peacefully at 281 local units out of 283 in province 3, 4 and 6.
The second round of polls in provinces 1, 2, 5 and 7 will be held on June 14.
Local-level elections could not be held after 1997 largely as a result of the decade-long Maoist insurgency that claimed more than 16,000 lives in Nepal.
Nepal has been witnessing political instability.
The Nepal government has tabled a new Constitution amendment bill in the Parliament to address the demands of the agitating Madhesis.
Madhesis, mostly of Indian-origin, launched a prolonged agitation between September 2015 and February last year against the implementation of the new Constitution which they felt marginalised the Terai community.