The incident occurred around 7.30 PM at about 200 metres away from the venue, where Balakrishnan was speaking at Nangarathupeedika in New Mahe area of Kannur, police said.
Balakrishnan left the venue shortly after the incident completing his speech, police said, adding the Democratic Youth Federation of India (DYFI) activist suffered injury in the incident.
"We strongly condemn this. The RSS' game plan is to expand their political base through such violence and communal polarisation which is their standard methodology. The supremely secular people of Kerala will, however, unitedly defeat such machinations," CPI general secretary Sitaram Yechury told PTI over phone.
Meanwhile, BJP has denied the charge, with its Kannur unit refuting the claims of CPI(M) that it was linked to the bomb hurling.
The politically sensitive district witnessed several violent incidents involving the RSS-BJP combine and the CPI(M) after the May 2016 Kerala assembly polls in which the LDF came to power.
In a recent incident on January 18, a 53-year-old BJP worker was stabbed to death at Andaloor in Dharmadam, the constituency of Chief Minister Vijayan, in which six CPI(M) workers have been arrested.
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