Ashish Ram of Raxaul in Bihar was killed as police opened fire on protesters at Shankaracharya Gate near Birgunj Customs, according to Home Ministry sources.
Ram received bullet shot in his head and was declared dead at the hospital.
The deceased was identified after a phone call was made to his maternal uncle from his mobile, police said.
Clashes erupted in different parts of Birgunj today after Nepalese police baton-charged Madhesi protesters, burned down their tents and evicted them from the Miteri bridge at the Indo-Nepal border, opening the main Birgunj-Raxaul border trading point for the first time in 40 days.
Violence in the area forced authorities to clamp an indefinite curfew.
Nearly 200 empty trucks stranded in the Nepalese side of the border were allowed to enter into the Indian territory during the brief period when the police took control of the area.
Several protesters were injured after police fired rubber bullets to maintain law and order.
Eight personnel of Nepal Police and Armed Police Force have also sustained injuries after agitators hurled stones at them.
Five protesters were arrested when the police intervened at around 4.30 am to open the Birgunj-Raxaul trading point through which about 70 per cent of bilateral trade is done, Home Ministry spokesperson Laxmi Prasad Dhakal told PTI.
Security personnel baton-charged about a dozen protesters who were sleeping in the tents set up on the bridge between Nepal-India border. The tents and beddings used by the agitators were burned.
Madhesis -- who claim to represent the interests of the Indian-origin inhabitants of Nepal's Terai region (plains) -- have been protesting close to the main trading point near Raxaul. Their agitation has led to a halt in supply of essential goods, causing acute shortage of fuel in Nepal.
Some three dozen Indian truck drivers, who were stranded on the Nepalese side of the border due to the blockade, had staged sit-in at the Indian Consulate office in Birgunj for the past few days seeking their return to India.
There is 15-km long queue of vehicles waiting for clearance from Indian authorities for entering into Nepal, Dhakal said.
These vehicles were carrying essential fuels, LPG, medicines and food items for supply to the landlocked country.
Indian officials have been saying that the supplies of essentials were stopped due to the blockade by the Madhesis.
Talks between Nepal government and Madhesi groups agitating over the country's new constitution on Sunday ended inconclusively, but Deputy Prime Minister Kamal Thapa said the dialogue was moving in a positive direction.
The major demands of the Madhesi Front are to re-draw the demarcation of the federal provinces and inclusion of more rights and representation to the Indian-origin Madhesi people.
Other demands include martyrdom status to those killed during recent protests, free treatment to the injured, compensation to victims' families and withdrawal of security forces from Terai districts among others.
The alliance has been staging protests in various parts of southern Nepal against the seven-province model of the newly-promulgated Constitution for more then two months.
The southern plains of landlocked Nepal have been simmering with tension since the Constitution was formally adopted on September 20.
Over 40 people have died in the violent agitation that has also overwhelmed Indo-Nepal ties as transit of goods and fuel to the Himalayan nation from India via the major border trading points has been badly affected.
Meanwhile, 12 trucks carrying petrol from China today entered Nepal through Rasuwagadhi trading point. These tankers were bringing 144,000 litres of petrol and diesel to Nepal for the first time following an agreement inked between Nepal Oil Corporation and Petro China in Beijing few days ago.
China has agreed to supply petroleum products to Nepal to fulfil one third of its demands, Nepalese Ambassador to China Mahesh Maskey told a television channel on Monday.
Under the agreement, China will supply petrol, diesel, LP Gas and air gasoline, he said.
China has announced to provide 1,000 metric tonnes of oil equivalent to 1.2 million litres to Nepal on grant basis as relief in the festival season.
Officials from Nepal Oil Corporation and Petro China will hold discussion on fixing prices for the petroleum products to be supplied to Nepal by China for long term consumption, he said.
Meanwhile, Prime Minister Narendra Modi expressed "shock" over the unfortunate killing of an Indian due to police firing in Nepal and requested for details from his Nepalese counterpart K P Oli even as India summoned that country's envoy over the incident.
"The prime minister has expressed shock and condemned the unfortunate killing of a youngster from Bihar due to police firing in Nepal," the Prime Minister's Office said in New Delhi.
During the telephonic conversation, Modi expressed concern over the incident and requested for details, it said.
19-year-old Ashish Ram of Raxaul in Bihar was killed after he received a bullet shot in his head when police opened fire on protesters at Shankaracharya Gate near Birgunj Customs, Nepal Home Ministry sources said in Kathmandu.
However, Modi assured the Nepalese leader that there was no obstacle from the Indian side on supply of fuel and other essentials.
"At the same time, the prime minister urged Nepalese leaders to work towards ensuring an early and effective solution to the crisis," the PMO added.
India also summoned Nepal Ambassador Deep Kumar Upadhyay and told him that it is "deeply concerned" over firing incidents in Birgunj.
He was also told that issues facing Nepal are political in nature and cannot be resolved by force and that the causes underlying the present state of confrontation need to be addressed by the government of Nepal credibly and effectively.
Earlier, the External Affairs Ministry Spokesperson said India has asked its freight transporters to exercise caution and not put themselves in danger. The advisory may deepen the supply crisis to the Himalayan nation.
He said Indian freight forwarders and transporters have voiced their worries again on Monday about the deteriorating situation across the border.
"We are advising them to exercise caution and not put themselves in danger. We are monitoring the situation carefully," he added.
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