The decision follows meetings between officials from both countries.
The border between Nepal's Rupandehi district and Uttar Pradesh's Maharajganj and Siddhartha Nagar districts was sealed Sunday for 40 hours.
The border checkpoints in Belahiya and Kakrahawa border were closed at 7 a.m. Sunday until 11 p.m. Monday.
Police said apart from emergency vehicles, no traffic will be allowed between the two countries during this period.
The Raxaul-Birgunj border crossing on the India-Nepal border in Bihar was closed for three days from Saturday evening.
Security officials from Nepal and India have been meeting even before the Indian parliamentary election started April 7 to discuss security matters.
Eighteen Lok Sabha constituencies in Uttar Pradesh and six in Bihar will vote Monday.