Indian Deputy High Commissioner JP Singh was present at the meeting between Jadhav and his family, which will last 30 minutes. Officials also said Jadhav's family would not interact with the media.
Shortly after the family of Jadhav met him, Mashal Malik, wife of Jammu and Kashmir Liberation Front (JKLF) chief Yasin Malik, in a video statement has said that while Pakistan was allowing alleged Indian spy Kalbushan Jadhav to meet his wife and mother on humanitarian grounds India has "kept her and her daughter from meeting Malik for the past three years".
The exact time of the meeting is not immediately known but officials said it would be around midday or early afternoon.
Kulbhushan's family, which travelled to Islamabad to meet him, would return shortly, as the meeting ended.
All the information about the meeting emerged through Pakistani foreign ministry tweets and images.
Pakistan alleges that Jadhav was involved in espionage and sabotage activities in Karachi and Balochistan. "Indian DHC in Islamabad will be the accompanying diplomat".
India, however, maintains that Jadhav was kidnapped from Iran where he had business interests after retiring from the Navy. TV footage showed a convoy of around seven vehicles escorting Jadhav's family in the city.
Police and paramilitary security forces including sharpshooters have been deployed at the MOFA to deal with any untoward security situation, they said.
The roads leading from and to the Foreign Office building have been closed to traffic ahead of the meeting. Special security passes were issued for those visiting the Foreign Office, the officials added.
He also confessed to working for India's spy agency, saying he was tasked with orchestrating acts of terrorism in Pakistan.
The Pak Military Court had sentenced Kulbhushan to death, but the matter is pending at the International Court of Justice (ICJ), which already stayed his execution.