Modi was scheduled to visit Janakpur, said to be the birthplace of Sita, Lumbini, the birthplace of Lord Buddha, and another sacred Hindu pilgrimage site, Muktinath, located in the southern mountainous region during his visit to Nepal to attend the 18th SAARC summit here on November 26-27.
Janakpur, Dhanusha, Mahottari and Sarlani districts were among the affected areas due to the shutdown.
Educational institutions and markets were partially closed and transport services also came to a halt. There were also anti-government rallies in parts of the city.
"We want Modi to visit Janakpur and his felicitation should be held in public at Barhabigha ground, not behind closed doors, as proposed by the ruling parties, Nepali Congress and CPN-UML," said Mahato talking to PTI.
The government was trying to dissociate Modi from the general public on the pretext of providing security to him, which is absurd, he said.
The agitators also burnt effigies of Deputy Prime Minister and Home Minister Bam Dev Gautam, who had said recently that Modi would not address public gatherings during the proposed felicitation programme.
Mahato alleged that efforts are on to create distance between Modi and the Madhesi people living in the southern plains of Nepal.
Earlier today, the Nepal government said that Modi's visit to Janakpur had not yet been officially cancelled despite reports about it being called off.
