Police said three buses, including a school bus, were stoned by unidentified persons on the outskirts of Puduchery town.
Cinema houses cancelled noon and evening shows, police said, adding, normal life was affected.
The bandh call was given after two of the five sisters, recently evicted by police from the Ashram residential quarters following a Supreme Court order, allegedly committed suicide with their mother by jumping into the sea.
Around 100 volunteers of the Puducherry State Youth Congress committee staged a dharna on the footsteps of the Assembly premises demanding a full-fledged probe into the suicide.
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The Rajiv Gandhi Municipal bus terminal in neighbouring Orleanpet wore a deserted look with privately run inter-state and intra-state and town buses being off the roads from early morning.
Activists of various parties, including CPI, CPI (M), CPI (M.L), RSP and the Forward Bloc, staged dharna at important junctions. Police removed them from the spot.
Police protection was stepped up at the Ashram and strict vigil is being maintained at all important junctions, police added.