The demonstrators, from southern lowland minority groups, are protesting against Nepal`s new constitution, which they say marginalises them.
Since August, this has sparked clashes around Nepal leaving dozens dead.
There were conflicting reports about the police crackdown on the protesters at the border. One report said police baton-charged demonstrators forcing them to remove the blockade, while another said authorities removed the tents of sleeping protesters and lined up trucks to pass through the crossing.
Police official Hobindra Bogati told the Associated Press news agency that more than 200 trucks and other vehicles had crossed from Birgunj in Nepal to Raxaul in India and more were lining up.
But, on the Indian side, thousands of trucks have not been able to cross over to Nepal for almost two months.
Reports said the trucks bringing fuel and other goods to Nepal were still blocked by Indian custom officials.
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