Minnie, 58, was found with a bullet to his head, but many people are refusing to believe the police version - that he took his own life at the farm of a friend near the coastal city of Port Elizabeth.
"The fact that the suicide note was found doesn't necessarily mean he wrote it willingly. I mean he could've written it under duress. The fact that he shot himself with someone else's pistol already raises questions," investigative journalist and author Jacques Pauw told South Africa's radio 702.
Minnie and journalist Chris Steyn co-authored The Lost Boys of Bird Island, which details shocking allegations against Magnus Malan, the once-powerful defence minister who was accused of setting up death squads and sanctioning military raids on neighbouring states as he fought to maintain white-supremacist rule in South Africa in the 1980s and 1990s.
In later years, Steyn confronted Malan about the allegations, and he replied: "What is a paedophile?", South Africa's privately owned News24 reported on its website. Aged 81, Malan died of a heart attack in 2011 - about 17 years after anti-apartheid icon Nelson Mandela swept to power as South Africa's first black president, heralding the end of the racist system of apartheid.
Malan was part of a regime which believed that the Bible justified racism - and they saw themselves as defending their faith, families, and race from being over-run by "godless communists" and "uncivilised blacks".
But secretly, Minnie alleged, Malan was part of a paedophile ring which raped boys - mostly of mixed race - during "fishing excursions" on Bird Island, a declared nature reserve near Port Elizabeth. The boys were flown to the island in military helicopters, made drunk during barbecues - and then sexually abused, he alleged. Malan's family and former colleagues strongly rejected the allegations against him, local media reported.
Other shocking allegations contained in The Lost Boys of Bird Island include:
• Some of the boys regarded Malan as an especially "cruel uncle", and nicknamed him "Ears" because of his big ears
• On one occasion, a gun was inserted into the anus of a boy. A shot was fired by Malan, and the critically injured boy was flown to a hospital in Port Elizabeth for treatment
• Men, dressed in suits, stood guard while the mixed-race boy was treated in the whites-only section of the hospital, even though this was illegal under South Africa's then-racial segregation laws
• The boy's family and the hospital matron were paid to remain silent.
Minnie said he had been building a case against Malan, but was forced to abandon his investigation after senior police officers in the regime, then led by Pieter Willem Botha, intervened and a prosecutor wrote in "fat red letters" on the docket: "Any investigation into this matter should be discontinued immediately."
The book alleged that the paedophile ring, which operated in the 1980s, included then-Environmental Affairs Minister John Wiley and wealthy businessman and diver Dave Allen. Minnie said he had, in fact, arrested Allen for allegedly having sex with children and for possessing child pornography.
Allen, Minnie added, had sung "like a canary", and dropped "a bombshell: he mentions a name. And not just any name, but the name of a very powerful cabinet minister.
"I'm taken aback, then he names two more cabinet ministers. He threatens to open the whole can of worms."
'Minnie feared for his life'
Allen never stood trial - he was found dead, at the age of 37, with a bullet wound to his head, just like the 60-year-old Wiley. Both died within weeks of each other in 1987. Both had, according to the official police version, taken their lives.
Now, more than 30 years later, Minnie - their nemesis - has died, also with a bullet wound to the head. Media captionWhat was apartheid? A 90-second look back at decades of injustice
As South Africa's Times Live news site put it: "That is the common denominator linking alleged suicides three decades apart that silenced three people with intimate knowledge of an alleged apartheid-era paedophile ring extending to the highest echelons of government."
Fuelling speculation that they were killed, journalist Marianne Thamm, who helped edit The Lost Boys of Bird Island, said Minnie had feared for his life. Minnie, who worked as a part-time teacher in China, said he had emigrated because a former contact in the security services had "handed me certain documents which was sufficient to convince me to leave the country", Thamm quoted him as saying.
'Body found near a bush'
At the time of his death, Minnie had been in South Africa to promote The Lost Boys of Bird Island. Its publisher, Tafelberg, said Minnie saw the book as "only the beginning of the process to have justice prevail for the victims whose stories are told in the book".
"Minnie had said nothing to Tafelberg to indicate that he would harm himself," it added in a statement posted on Twitter. Tafelberg Publishers were shocked to hear of the sudden death of #MarkMinnie, co-author of The Lost Boys of #BirdIsland, one week after the release of the book. #Tafelberg’s last contact with Minnie was on Sunday night, but he had been out of reach since Monday morning.
So far, the police have only said that Minnie was found by a friend "lying near a bush with a gunshot wound to his head. A firearm was found lying next to him".
"At this stage no foul play is suspected. Police have opened an inquest pending the results of the post-mortem," a police statement added.
If it does turn out that Minne was killed, it would imply that hit men - loyal to the former regime - are still operating in South Africa. And that would strike fear into the hearts of many people - not least other potential whistleblowers.
But Steyn, the co-author of The Lost Boys of Bird Island, said she would press ahead with investigating alleged paedophiles in the former regime.
"He [Minnie] would have wanted me to continue and that is exactly what I'll be doing," she was quoted by South Africa's IOL news site as saying.