The incident took place yesterday in Kokrajhar's Rabindra Nagar.
Kokrajhar police officials rushed to the spot as soon as the locals informed the police and the matter is under investigation.
The incident follows a similar act of vandalism in Kolkata where a bust of the Jana Sangh leader was damaged on March 7, for which seven people were arrested.
This is the first such case in Assam after a statue of Communist leader Vladimir Lenin was toppled in Tripura town two days after the Bharatiya Janata Party (BJP) swept the Left Front out of rule on March 3.
Mukherjee's bust in Kokrajhar was reportedly inaugurated in 2002 by BJP leader and former Bihar Minister Kailashpati Mishra. (ANI)