The grim discovery came as part of investigations into misdeeds committed under Bashir, who ruled the country with an iron fist before the army deposed him amid huge street protests in April 2019.
A investigating committee "found the mass grave in the past four days after hearing witness accounts”, about killings at Ailafoon military camp, Public Prosecutor Tagelsir Al Hebr told reporters in Khartoum.
Some of those suspected of involvement in the incident have fled the country, said Hebr, who did not disclose how many bodies were found.
"The grave was exhumed and now the committee will continue to work with forensic authorities and examine the evidence,” said Wael Ali Saeed, a member of the investigation committee.
Ailafoon military camp, located southeast of the capital Khartoum, was used for training new conscripts under Bashir’s rule.
In 1998, a group of conscripts died as they attempted to escape the base for the Muslim Eid Al Adha holidays.
The Sudanese government said at the time that around 55 young conscripts who fled the base drowned when their overloaded boat capsized in the Blue Nile.
Opposition groups accused the regime of deliberately killing the conscripts and reported a death toll of more than 100.
Other investigations
Many Sudanese families reported that their sons went missing and their remains were never found.
Bashir used conscripts in the civil war against rebels in the oil-rich south, which seceded in 2011.
Following Bashir’s ouster last year, the country has since August been led by a civilian-majority administration presiding over a three-year transitional period.
Sudanese authorities have vowed to probe "violations” committed under Bashir as well as violence during last year’s protests against his rule.
Hebr also disclosed on Monday that an investigatory team is looking into the 1989 Islamist-backed military coup that brought Bashir to power.
Other ongoing investigations include cases of corruption and violence against demonstrators during anti-government protests that took place from December 2018, he added.
Doctors linked to Sudan’s protest movement said at least 246 were killed and hundreds others wounded during the 2018-19 protests.
Since his ouster, Bashir and many of his aides have been kept in Khartoum’s Kober Prison on multiple charges.
In December, he was sentenced to two years detention in a correctional facility in an initial corruption case.
The ex-president has for a decade been wanted by the Hague-based International Criminal Court (ICC), where he faces charges of genocide and war crimes committed in the war ravaged Darfur region of western Sudan.
The Darfur conflict, which erupted in 2003 between African minority rebels and Bashir’s forces, killed 300,000 people and displaced 2.5 million others.
Last week, top militia leader Ali Kushayb, who was accused of atrocities in Darfur, handed himself over to the ICC