He inaugurated the programme at a primary health care centre in neighbouring Nellithope constituency.
The day-long programme is aimed at covering 91,500 children in the whole of the Union Territory.
Mobile teams comprising medical personnel were operating at various points, including border villages to cover children travelling in buses and other vehicles.
Special booths were set up in Puducherry, Karaikal, Mahe and Yanam regions to carry out the immunisation.
Puducherry Health Minister Malladi Krishna Rao and officials of the directorate of Health and Family Welfare Services were present.