The arrests were made yesterday and the fishermen were brought to provincial capital Karachi.
The Pakistan Maritime Security Agency (PMSA) during an operation in open sea off Karachi confiscated 12 Indian launches and arrested 100 fishermen, Radio Pakistan reported.
According to reports, the launches have been confiscated for violating Pakistani coastal territory.
However earlier, a PSMA spokesman had said that 70 Indian fishermen had been arrested in Pakistani waters.
"We arrested 70 fishermen yesterday," Lt Commander Wajid Nawaz told PTI.
Both countries regularly arrest fishermen who stray in to each other's waters due to poorly marked sea boundary.