Pakistan High Commission press attache Manzoor Ali Memon said Gul Bahar was arrested July 23 in Harani Dhoro area off Sir Creek.
He said the high commission lodged a protest with Indian authorities Tuesday.
He said Pakistan had sought consular access to the arrested fisherman and sought a probe into the incident.
"The incident can vitiate the atmosphere, especially at a time when both sides have embarked on move for normalization of relations," he said.
The Indian external affairs ministry could not be reached for comment.