The first phase of the election in the land-locked Nepal was held on November 26.
The decision was made by the government to seal the border after holding meetings of security officials of both the countries.
The second phase of the elections is taking place in 45 districts on Thursday.
Following the government's move to seal the border a large number of people travelling to India from Nepal and vice versa have been stranded in the Kakarbhitta border point.
"The border is open for those traveling to India," Bhattarai added.
Residents of Bhadrapur, Nepal's eastern border with Bihar state, are facing difficulties due to the decision to seal the border, the officer said.
Similarly, entry points along the Nepal-India border in Kailali district have been sealed for 72 hours in view of the elections. The Indo-Nepal border will open on Thursday evening.
Silent period has started ahead of elections from today when candidates are restricted to conduct any type of election campaign.
The elections are being seen as the final step in Nepal's transition to a federal democracy following a decade-long civil war till 2006 that claimed more than 16,000 lives.
While many hope Nepal's first state elections will hasten regional development, others fear they will spark a fresh wave of violence.
In 2015, when Nepal adopted a new Constitution that split it into seven states, dozens of people were killed in ethnic clashes over territory and rights.
Violent clashes not only left more than 50 people dead, but also left the country with severe shortages of fuel and medicine because protesters blocked the borders with India.
The protesters finally agreed to the elections after some amendments were made to the Constitution.
The polls are taking place under a new Constitution passed by lawmakers in September 2015 as part of a peace process that began with the end of a decade-long civil war.
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