The party was leading in 41 constituencies while its rival CPN-UML was ahead in 30 seats.
The Prachanda-led UCPN-M, which had emerged the largest party in the last election in 2008, was in third position with a lead in just 10 seats.
Madhesi Janadhikar Forum was leading in six constituencies.
Former Prime Minister Baburam Bhattarai of the UCPN-M was well ahead of all his rival in a seat in Gorkha district while party chief Prachanda had taken the lead in Siraha but was lagging behind in Kathmandu.
The counting will lead to the formation of a 601-member assembly to draft a new Constitution, including 240 elected under a direct voting system. There was proportionate voting for 335 seats and the remaining 26 members will be nominated by the government.
The counting began even as ballot boxes from some remote areas were still being ferried to district headquarters. Ballot boxes from mountainous districts like Humla, Kalikot, Mugu, Mustang, Taplejung, Gorkha and Jajarkot were transported by helicopters, the Election Commission said.
People voted amidst tight security, with 200,000 security personnel, including 60,000 soldiers, deployed across the country yesterday. Voting was held at 18,438 polling centres.
Voting at a polling booth in Depal village of Jumla district was disrupted due to unfavourable environment. The re-polling will be done on November 22, according to the EC.
In the previous Constituent Assembly elections in 2008, UCPN-M had emerged as the largest party with Nepali Congress and CPN -UML in second and third place.
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