The officers were executed in mysterious circumstances after a quick military trial one year after Bashir himself took the power in a military coup in 1989. There burial site was not disclosed for decades.
"The public prosecution managed to find a mass grave that data indicates that it is most likely the graveyard where the bodies of the officers who were killed and buried in a brutal manner," the public prosecutor said in a statement.
A team of 23 experts reached this result after an effort that lasted for three weeks, and more forensic and investigative measures will be taken in the site, the statement added.
The public prosecutor assured the families of the executed officers that "such crimes will not pass without a just trial."
Bashir appeared in court on Tuesday at the opening of his trial for leading the military coup that brought him to power in 1989. He was ousted by the army in April 2019, after months of mass protests.
Bashir's attorneys could not immediately be reached for comment.
Local media reports said earlier this month that prosecutors questioned Bashir over the 1990 executions. The prosecution has not publicly commented on the matter.
Last month, Sudan's public prosecutor announced the discovery of a mass grave east of Khartoum suspected to contain the remains of students killed in 1998 as they tried escaping military service at a training camp.
Bashir already was handed down a two-year sentence by a court in December on corruption charges. Bashir also faces trials and investigations over the killing of protesters.
He is also wanted by the International Criminal Court (ICC), which issued arrest warrants against him in 2009 and 2010 on charges of genocide, war crimes and crimes against humanity in Sudan’s restive Darfur region.