US intelligence flagged the Guptas' dubious activities as far back as 2009, resulting in an investigation by South African intelligence agencies that concluded that the family was a threat to national security.
As the full extent of the state capture project unfolds at the Zondo commission of inquiry, new details have emerged about how the heads of SA's intelligence agencies tried to caution former president Jacob Zuma that his relationship with the Guptas was undermining national security.
Former spy bosses Gibson Njenje, Moe Shaik and Mzuvukile Jeff Maqetuka were alarmed to learn in the course of their investigation about the scale of the Guptas' involvement in Zuma's very first cabinet reshuffle in October 2010.
Now, for the first time, Njenje and Shaik have broken their silence, giving the Sunday Times a blow-by-blow account of their investigation of the Guptas.
They were forced out of the public service in 2011 after a breakdown in relations with then state security minister Siyabonga Cwele, who called their Gupta probe "irregular".
Njenje and Shaik said they had several meetings with Zuma, but quit when they realised he would not act on their warnings.
The Sunday Times has also learnt that former communications minister Siphiwe Nyanda was fired to give the Guptas access to the communications sector, particularly the SABC.
Nyanda has for the first time revealed that after he rebuffed attempts by the Guptas to meet him, Zuma removed him as communications minister and appointed Roy Padayachie, a close ally of the family. During Padayachie's tenure, Atul Gupta and Sahara Computers were given special recognition by the ministry as tech industry leaders.
Under Padayachie, Hlaudi Motsoeneng began his ascent at the SABC and signed the broadcast agreement for the New Age business breakfasts - at no cost to the Guptas.
Njenje, the former head of the National Intelligence Agency, told the Sunday Times he received a request from his US counterparts in 2009 wanting to know about the Guptas' interest in uranium mining. This was as the Guptas' Oakbay Resources was acquiring Uranium One's Dominion mine, which they renamed Shiva Uranium.
Enriched uranium is a critical component for both nuclear power generation and military nuclear weapons.
"The Americans wanted to know why the Guptas are interested in mining uranium and where they intend sending their product. Naturally we were interested as well," said Njenje.
Shaik, the former head of the South African Secret Service, confirmed the request from the US's Central Intelligence Agency. An acting spokesperson at the US embassy in Pretoria, Carrie Schneider, said: "As a policy, we never comment on intelligence matters."
The investigation by the South African intelligence agencies, based on open source information and interviews, threw up alarming information about the family's activities and relationship with Zuma.
Njenje said: "In 2010 they started flexing their muscle and their links with the president.
"They were talking to ministers, directors-general and senior officials. From a state security point of view, we were trying to find out why this audacity. They were making an open show that they have a relationship with the president.
"We got to know the president was visiting the Gupta compound [in Saxonwold, Johannesburg] at least once a week. Every Monday, on his way from meetings at Luthuli House, he would stop there for dinner."
Njenje said they also learnt that the Guptas were in charge of arrangements during Zuma's state visits. This was particularly the case during the June 2010 state visit to India, and to China two months later.
In her testimony at the state capture inquiry this week, former ANC MP Vytjie Mentor mentioned the Guptas' unusual role in protocol arrangements for the China visit.
Njenje said one of the major issues of concern to them was the interference of the Guptas in Zuma's first cabinet reshuffle in October 2010.
Zuma replaced seven ministers in the reshuffle, axing Nyanda as communications minister, Barbara Hogan as public enterprises minister and Makhenkesi Stofile as sports & recreation minister.
Mentor testified that Ajay Gupta told her Hogan would be fired and offered her the public enterprises ministry if she canned the SAA route to Mumbai. Mentor said she became "agitated" and declined the offer and that Zuma walked into the room and tried to pacify her. Malusi Gigaba, now home affairs minister, was appointed in Hogan's place.
Shaik said they were alarmed when they found out that people were being "summoned" by the Guptas in connection with the reshuffle. He said they were also disturbed when Zuma appointed people who were perceived to be close to the Guptas in the cabinet.
Nyanda told the Sunday Times he was "taken by surprise" by his axing.
"In retrospect it all makes sense. We were the first victims of these series of Gupta purges," he said.
Zuma reshuffled his cabinet 11 times.
Nyanda is a former chief of the South African National Defence Force and was the chief of staff of the ANC's military wing, Umkhonto weSizwe.
He said during his tenure as communications minister, he received a visit at his office from Duduzane Zuma, accompanied by the Gupta brothers.
"They said they were just introducing themselves as they were doing business in the communications space. I paid no heed at the time as I met many people in the industry."
He said he was subsequently told by people working in state-owned entities under the department of communications that the Guptas wanted a meeting with him.
"They were going via other people who were trying to arrange for those guys to see us, but I did not respond," said Nyanda.
Nyanda said that during a weekend at the end of October 2010, he was in Durban when he received a call from the presidency asking him to come to a meeting with Zuma. Nyanda said he would only be back that Monday.
He then received a call from Zuma, who informed him that he was being removed as minister. Zuma offered to appoint him ambassador to Germany. Nyanda declined.
He said he insisted on meeting Zuma to find out the reasons for his axing.
"At the time, there was a story that I was running a security company and monitoring his affairs. I asked the president if he believed I was a threat to national security and intercepting communications because I should face criminal prosecution if I was," said Nyanda.
"He said no and told me something about the SABC. I asked what about it … To be honest I found very little joy in that interaction," said Nyanda. He said he only realised later that Zuma wanted the SABC "under the control of his cronies".
Nyanda said he declined an offer by Zuma to become his economic adviser and remained as an ANC MP. "My enthusiasm for anything ANC and government really died. I was just going through the motions."
Nyanda, Njenje and Shaik were signatories to a public statement in May 2016 by 27 former directors-general calling for an independent public inquiry into state capture.
All three say they are willing to testify at the Zondo commission if called.
Nyanda said he would be willing to give evidence that he was at an ANC national executive committee meeting when Fikile Mbalula made an emotional declaration that the Guptas had told him he would replace Stofile as sports minister. "[Zuma] didn't say anything after such a serious allegation by Mbalula. He didn't address it at all," said Nyanda.
Njenje said he, Shaik and Maqetuka had gone to see Zuma several times about their concerns about the Guptas.
"The president gave us a story about Duduzane and Duduzile and the Guptas that we never really understood. It was clear he was not going to do anything," said Njenje.
Shaik said Zuma's response to their serious warnings made them despair.
"He said the Guptas were the only people willing to help his son," said Shaik...