Such a special prayer was held at Panaji's Immaculate Conception Church on Saturday.
He is currently undergoing treatment at Mumbai's Lilavati hospital since Feb 15.
Lord Hanuman Shree Maruti Temple in Dhavem village in Sattari taluka, 45 km from Panaji, was the first to perform a puja, where hundreds of villagers recited the 'Mahamrutyujay Mantra Jaap', a prayer from the Rigveda.
"We have begun reciting the mantra, which will continue for two days. We will continuously chant the mantra seeking God's blessing for the health of our chief minister," villager Rama Marathe, who is taking part in the recitation of the prayer, said.
"We are sure that Parrikar will be back in the state soon as we need him. He is a chief minister who is connected to the masses. He has touched the life of every person in the state," he said.
In Vasco town, 40 km from here, United Taximen Association, a union of the black-yellow taxi operators working at Dabolim airport, held a puja at the Shree Damodar temple for Parrikar's recovery.