Traffic movement in the capital was disrupted in the vicinity of Singhdurbar, the main administrative complex of the country, for hours due to the protest.
About 2,000 protesters carrying placards with anti- government and pro-Madhesi slogans gathered at Singhdurbar and Nayabaneshwor areas, an hour before the government offices opened.
They forcefully tried to enter the prohibited areas, triggering a scuffle with riot police who were deployed to guard the important government offices.
Chairman of Federal Socialist Forum Nepal, Upendra Yadav led the protests at Maitighar Mandala and Sadbhawana Party Chairman Rajendra Mahato at Hanumanthah.
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There was heavy presence of security personnel in the area since early morning to prevent any untoward incident.
The major demands of Madhesis, mostly of Indian-origin, include re-demarcation of the seven province model of federal structure, inclusiveness and proportionate representation of marginalised groups and ethnic minorities including the Madhesis, indigenous groups and dalits in all the state bodies.
The alliance started their Kathmandu-centric fresh protests yesterday.
Madhesis earlier had launched six-month-long agitation from September to February in which more than 50 people were killed. The agitation had also crippled the landlocked country's economy as supplies from India were blocked.
The alliance has this time changed its strategy and focused on capital city in an attempt to draw attention of the government and other stakeholders to their demands.
The United Democratic Madhesi Front (UDMF), an alliance of seven Madhes-based parties, accused Prime Minister KP Sharma Oli's government of using excessive force to suppress their agitation demanding more constitutional representation.
"Government is not serious enough to address the issues raised by the agitating Madhesi parties through dialogue," the Front had said.