The government has filed treason charges against the trio, who were involved in holding referendum in southern Nepal on whether to declare the southern plains - home to the Indian-origin Madhesis - as an independent state or not.
The three were arrested from Siraha district in southern Nepal on January 2 and brought to Kathmandu, where charges have been filed against them in the Special Court, according to officials.
Among the three, Chandeshwor Mahato, 60, acted as an international observer and Sudip Raj Kushwaha, 26, as the Election Officer in the mock referendum held on December 26 in Siraha district.
The arrest comes in the wake of intensified action by the government against those propagating for a free Madhes.
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Brajesh Singh and Sadam Ansari, arrested on November 24 from a meeting, are still in police custody, the Alliance for Independence Madhes in a statement.
Those arrested for conducting the mock referendum are believed to be the followers of C K Raut who who returned Nepal from the US five years ago.
Unlike the Madhesi Front which is demanding re-demarcation of the provincial boundary, the Alliance for Independent Madhes wants the southern plains adjoining India as a separate state.