The protest turned violent at Jaigaon in Alipurduar district when police stopped a rally by protesters, injuring many including police personnel.
Police fired rubber bullets and used tear gas to stop the GJM supports.
The protesters demanded centre's intervention for the cause of Gorkhaland.
Earlier on Saturday, several protestors and police personnel were injured in the clashes that took place in Sukna area of the hills.
The police and security forces patrolled the streets of the hills and kept a tight vigil at all entry and exit routes.
Normal life remained crippled on the 46th day of the ongoing indefinite strike to press for a separate Gorkhaland state. Barring medicine shops, business establishments, restaurants, hotels, schools and colleges remained closed.
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