A dawn-to-dusk shutdown was called across Arunachal Pradesh by the powerful All Arunachal Pradesh Students Union (AAPSU).
Violence was reported from several parts of the state including state capital Itanagar where public transport vehicles came under attack. At least four state-owned buses were damaged and several private vehicles were attacked.
The protesters even pelted stones on the police personnel.
The state BJP head office at Itanagar was also ransacked, police sources added.
Chakmas and Hajongs came to India and are settled in several states of Northeast India as refugees.
They fled Chittagong Hill Tracts in Bangladesh, having lost their homes and land to the Kaptai Dam project on Karnaphuli River in the mid-1960s.
Like the Rohingyas of Myanmar, they too face religious persecution.
While Chakmas are mostly Buddhists, the Hajongs are largely Hindus.
In Arunachal Pradesh they have colonies in Subansiri, Lohit and Tirap districts.
The communities are finally set to get limited citizenship in India, but officials say they cannot be given land or tribal rights as that may trigger conflict.
The chief minister of Arunachal Pradesh Pema Khandu, where most of the refugees live, has said such a move would change the demographics of the state which has a predominantly tribal population with special rights including over land.
The decision to grant citizenship to the Chakma and Hajong also comes as India is under fire for its plan to deport some 40,000 Rohingya Muslims who face persecution in Myanmar.
(With inputs from Reuters)