Allegations of bribery have dogged the governments of both President Jacob Zuma and Thabo Mbeki.
Mr Zuma announced the investigation in 2011. His former financial advisor Schabir Shaik was convicted of corruption over the 1999 deal.
Mr Zuma was also charged but the case was dropped before he took office.
His supporters have always maintained that he had been the victim of a political smear campaign.
Mr Mbeki is among those expected to be called as a witness.
The huge deal – post-apartheid South Africa’s largest such transaction – was intended to modernise its national defences.
It involved companies from Germany, Italy, Sweden, Britain, France and South Africa.
But corruption allegations swirled around the deal from the start.
Another official, Tony Yengeni, who was the chairman of parliament’s defence committee at the time of the deal and the chief whip of the governing African National Congress, was convicted of fraud in 2003.
He was freed from prison on parole in 2007, after serving five months of a four-year sentence.
His sentence was cut on appeal and further reduced by a general amnesty.
Shaik was jailed for 15 years in 2005 for soliciting a bribe from Thint, the local subsidiary of French arms company Thales.