However, the protesters were swiftly removed by security personnel after policemen rushed to cover the protesters with blankets and took them into custody.
"The main gate leading to the secretariat has been shut for the time being to prevent protesters from entering the premises and security arrangements have been intensified in the area," said an officer.
DCP Amanjit Kaur told reporters that all three protesters have been arrested and necessary measures taken to prevent recurrence of such incidents.
Protests against the Bill have enveloped virtually the entire north-eastern region since the Bill was passed in the Lok Sabha on January 8.
The Bill seeks to provide Indian citizenship to six non-Muslim minority groups from Pakistan, Afghanistan and Bangladesh. The fear in the northeast is that if this is done, "outsiders" will overwhelm the locals in the region.
A senior KMSS member said, "We hope that the protest shames the government and the bill is immediately revoked."
A nude protest was also staged last month by 10 Assamese youths in front of Parliament as well as in Jorhat and Tinsukia districts of Assam.
The Citizenship (Amendment) Bill, passed by the Lok Sabha on January 8, seeks to grant Indian citizenship to non-Muslims who fled religious persecution from Bangladesh, Pakistan and Afghanistan, and entered India before December 31, 2014.
Protests against the bill have rocked the entire northeast over the past five weeks, with several organisations and political parties vehemently opposing it.
(With PTI inputs)