Sartaj Aziz, advisor to Sharif on National Security and Foreign Affairs, told parliament on Friday that there were 491 Indian prisoners, including 437 fishermen and 54 other civilians, in jails across Pakistan.
He said nine of detainees were already set free and there is proposal to release another 73 Indian fishermen.
Aziz said the latest list given by India on July 1 under Consular Agreement showed that there are 386 Pakistani prisoners in Indian jails.
But according to the record of the Pakistan Foreign Office, there were at least 485 Pakistanis jailed in India, including 172 fishermen and 313 other civilians, he said.
This shows a total of 99 Pakistanis in India are unaccounted for, he said.
"We have taken up the matter with the Indian authorities to clarify the discrepancy," Aziz said in reply to a question by one of the members.