Public vehicles remained off the roads while major markets and educational institutions were forced to shut down in Kathmandu and other major cities in the strike called by hardline CPN-Maoist (Chand), led by Netra Bikram Chand.
Hundreds of security personnel were deployed in Kathmandu and surrounding areas to prevent violence during the protest, the first national strike since a devastating quake hit the country in April.
The agitating activists torched several vehicles during the protest, police said, adding that no casualties had been reported so far.
The nation-wide strike was called to oppose the Constitution drafting process initiated by the four major political forces, the Nepali Congress, CPN-UML, UCPN-Maoist and Madhesi Peoples Rights Forum Democratic after inking a 16-point deal.
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Nepal's Maoists struck a deal with rival parties on the new Constitution last month after years of bitter disagreement.
But the breakaway faction of the party said the deal betrays the principles of the Maoists, who fought a decade-long civil war with the state that ended in 2006 and led to the abolition of a centuries-old feudal monarchy.
The Maoist activists were also opposing an agreement between India and China to boost border trade at Qiangla/Lipu-Lekh Pass, close to an area which Nepal claims to be part of its territory.
Lipu-Lekh Pass, the last point of Nepal's border with China and India and known as an ancient route for traders and pilgrims transiting between Nepal and Tibet, is a far western point, near Kalapani, which is a disputed border area between Nepal and India.
During Prime Minister Narendra Modi's China visit in May, India and China agreed to expand border trade at Lipu-Lekh Pass.
The strike also crippled life in Lalitpur, Bhaktapur, Banepa, Palpa and Hetauda.