The death of Nawab Akbar Khan Bugti, 79, a former political governor, on Saturday sparked violent protests in the southwest province of Baluchistan.
Bugti was killed when the cave he was in collapsed during fighting with government forces who had earlier attacked his hideout in the hills of Pakistan's poorest and least populated province.
Major-General Shaukat Sultan, a spokesman for the military, said on Thursday that Bugti's "badly crushed" body had been retrieved from the rubble and was in an "advanced state of decay".
A senior local official said Bugti will be buried at his ancestral home on Friday.
That event will be subject to strict security measures after violence has flared in Baluchistan in recent days.
Four days of rioting followed Bugti's death, leaving 10 dead and banks and other buildings burnt out.
Reports have suggested authorities would move to restrict the number of mourners at the funeral after trouble flared after funeral prayers on Tuesday.
Supported by a heavily armed private militia, Bugti had spent years fighting the government for provincial autonomy and a greater share of the profits from the region's natural resources, including gas, gaining him great respect among the local population.
Bugti's death has provoked
violent protests in the region
Opposition parties have demanded an inquiry into his death, and the length of time it has taken to recover his body has added to speculation over the official account of his death.
The government says its security forces did not intend to kill Bugti in the weekend operation 265km east of Quetta, the provincial capital, which left more than 20 people dead.