The man found dead in Landhi jail was identified as Kishore Bhagwan. His body was moved to a nearby hospital.
Indian diplomatic sources told PTI that they had been informed by the Foreign Office in Islamabad about the death of the prisoner but the cause of death was yet to be ascertained.
Indian authorities have sought additional information.
On December 19, Indian fisherman Bhikha Laka Shival, 35, died in a jail in Karachi and the cause of his death too is yet to be established.
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"We are likely to receive the body (of Shiyal) soon. We would be making arrangements for the mortal remains to be sent back," an Indian diplomat said.
The Indian government has approached Pakistani authorities to speed up the process of sending back Shiyal's body, which has been kept in a morgue.
Bhagwan was among more than 50 Indian fishermen arrested for allegedly entering Pakistan's Exclusive Economic Zone in January last year. He escaped from jail a month later while cleaning the main gate of the facility.
He was recaptured in December last year. Pakistani media reports quoted police as saying that he lived on the roads of Karachi after his escape.