Sashastra Seema Bal (SSB) Director General Archana Ramasundaram said the border guarding force has also ordered a fact-finding inquiry to be conducted by a Deputy Inspector General (DIG)-rank officer of the force.
"Our troops have told us that there has been no firing from their side but as the allegations are serious, I have ordered for a Court of Inquiry," she told PTI.
"The situation is tense today and a large number of Nepalese people have gathered on the spot again and resorted to shouting anti-India slogans and stone-pelting. Local officers and SSB officers are on the spot," it said.
The Ministry of External Affairs has said India has sought from Nepal the post-mortem and forensic reports of the Nepalese national who is alleged to have been killed in SSB firing.
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The SSB said the clashes were first triggered on Wednesday when some "Nepalese people gathered near pillar no 200" in the Basai area of Pilibhit in the said district and tried to construct a culvert.
"They were stopped from doing so as earlier the authorities from both sides had agreed to allow construction of culvert only after conducting a joint geological survey.
"But yesterday, again in the morning, a group of Nepalese people gathered at same site and started pelting stones on SSB personnel and local police and administrative authorities on duty," it said.
While the local police fired a teargas shell, two were fired by the Nepal police to "disperse the crowd" yesterday, it said.
The situation, the SSB said, was brought under control by the intervention of the District Magistrate and Superintendent of Police of Lakhimpur Kheri and Nepalese authorities in Kanchanpur.
Officials said the SSB is yet to get the post-mortem report of the deceased youth and there are reports that suggest that he might have died due to some liver ailment.
"However, official reports in this regard are awaited," they added.
Uttar Pradesh shares a 599.3 km long open border with Nepal touching seven districts- Pilibhit, Lakhimpur Kheri, Bahraich, Sravasti, Balrampur, Sidhharthnagar and Maharajganj.