The fishermen, who have been released by the country's northern Mannar court, were detained by the Sri Lankan Navy December 19.
The new arrests comes a day after the Navy arrested 43 Indian fishermen and seized six fishing trawlers in seas Southeast of the Delft Island in Jaffna.
Fishermen from both countries are arrested frequently for inadvertently trespassing into each other's waters.
Over 10 boats suffered damage to some extent after being hit with stones, the association leader said, adding that the fishermen returned to shore following the incident.
Most of the fishermen were imprisoned after crossing over to the Pakistani waters four to five years ago.
The Edhi Trust Foundation, a non-profit social welfare organisation, has made arrangements to safely transport the 20 Indian fishermen to the Wagah border.
Near Neduntheevu late Monday night, a Sri Lankan naval vessel rammed into Indian fishermen's boat, throwing three of the occupants into the sea in the impact.
Hundreds of fishing boats carrying black flags reading 'save our fishermen' were launched in the protest action launched from the northeastern region of Mullaithivu to the Point Pedro in the north.
The Sri Lankan Navy arrested the fishermen off the coast of Vettilaikeni in the northern province's point Pedro area.
The incident happened late on Wednesday near Katchatheevu when Lankan Naval personnel, who came in about 10 patrol boats, hurled glass bottles and stones, officials said.
On Sunday evening, they were trawling along with a few other boats about 40 nautical miles southeast of Kodiyakarai when the incident happened around 4 pm.
Twenty-four Indian fishermen were arrested by the Sri Lankan Naval personnel today for allegedly crossing the International Maritime Boundary Line.