The protesters demanded a probe by the National Investigation Agency (NIA) against the politburo member for the alleged remarks made by him at a recent meeting of the CPI(M) Alappuzha district committee.
The activists, including women, were led by BJP Thiruvananthapuram district president Suresh Kumar.
They were stopped by police near the CPI(M) leader's house.
The workers later dispersed, the police said.
BJP has in a complaint to the DGP stated that a case should be registered against Balakrishnan for "constitutional violation and sedition."
Balakrishnan's statement would hurt the country's unity and integrity and was "serious," it has said.
The CPI(M) leader's remarks amounted to "challenging" and "insulting" the Indian Army, who are trying to check the Chinese threat in the Doklam region, it added.
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