South Africa's Public Protector Busisiwe Mkhwebane said she would probe alleged "improper or dishonest" acts and "unlawful enrichment... By certain public officials" at rail company Prasa, power company Eskom and the Transnet freight logistics conglomerate.
One of the allegations involves suspected kickbacks worth 5.3 billion rand ($411 million) on a contract to purchase locomotives from China for Transnet, Mkhwebane said in a statement late Wednesday.
Brian Molefe, a close Zuma ally and a former head of Eskom, is among the people who will be investigated.
A report published last year by the state ombudsman accused the Guptas of wielding unprecedented influence over the government, including letting them select ministers.
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It also ordered a judicial inquiry into the allegations, but Zuma has opposed the inquiry and launched a court challenge against the report. His challenge will be heard in October.
The Democratic Alliance, the main opposition party, today criticised the probe for being too narrow and not focussing on Zuma.
In power since 2009, Zuma has been engulfed by graft scandals and several humiliating court rulings while grappling with record unemployment and a sluggish economy.
His ruling African National Congress (ANC) party welcomed the decision to investigate the claims contained in the emails.
"We trust that the investigation will shed some much needed light on the disturbing allegations which, if left unattended, have the effect of undermining the integrity and credibility of our government and state," the ANC said.