Ministry spokesperson Rudi Urip said that the latest figure was provided by the Indonesian task force that manages domestic Hajj pilgrims, the PPIH.
"The total Indonesian casualties consisted of 86 who departed from Hajj embarkation points across the country and five Indonesian nationals working in Saudi Arabia," Rudi said in the ministry's premises, Xinhua reported.
The fatality figure was a sharp rise from 59 recently announced by the PPIH, he added.
The PPIH has been coordinating with related offices under the supervision of the Indonesian foreign affairs ministry to search for other Indonesians that had possibly been killed in the crush.
Indonesia sent more than 168,000 Hajj pilgrims to Saudi Arabia this year.