Kulbhushan Jadhav will now undergo trial under charges related to terrorism and sabotage, Pakistan's daily newspaper Dawn reported.
In December, Jadhav's mother and wife had met him in prison, however, it resulted in a huge row between India and Pakistan after authorities confiscated his wife's shoes.
Pakistan officials later sent the shoes for a foresnic check as the family meeting blew up into a full-scale diplomatic row between India and Pakistan.
The Dawn newspaper quoting Pakistan officials reported that Jadhav has multiple cases against him in which he had been indicted on terror-and sabotage-related charges.
Jadhav was captured by Pakistani security forces on March 3, 2016, in Balochistan.
The Indian national was sentenced to death by a Field General Court Martial (FGCM) in Pakistan in April last year.
However, the International Court of Justice on May 18, 2017, stayed the hanging after India approached it against the death sentence.