The protests come at a time when the construction work on the Rs 594-crore project in an area of around 100 acre near Chengalpattu is under progress.
Locals allege the facility would be hazardous for the health of the people living nearby.
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They also complained they were not clearly told about the project and were earlier informed that a fertiliser manufacturing firm was coming up on the land.
They claim they came to know that the land was allotted for vaccine manufacturing facility only at the time of bhumi puja.