A spokesperson for the agency said that the fishermen were repeatedly warned to leave Pakistan's territorial waters.
"They were violating Pakistan's territorial waters by fishing illegally in our area in the open sea," he said.
The spokesperson added the fishermen were arrested from near Sir Creek, along the maritime border between Sindh and Gujarat.
He said that police have registered cases against the Indian fishermen under the foreign and fisheries acts of the law.
Pakistan and India frequently arrest fishermen as there is no clear demarcation of the maritime border in Arabian sea and these fishermen don't have boats equipped with the technology to know their precise location.
Although both countries have frequently released these fishermen from jails as goodwill gestures but according to official figures still more than 300 Indian fishermen are currently languishing in Karachi prisons.