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The arrest happened even as the country's leading journalists were meeting in the Avusa newspaper house building to discuss the proposed media law clampdown, under the aegis of Sanef (the SA National Editors Forum).
Sunday Times laywer Eric van den Berg was present when the arrest happened.
Sapa reports that Wa Afrika was arrested for fraud and defeating the ends of justice.
Police Hawks spokesman Musa Zondi confirmed the journalist had been arrested and would appear in court within 48 hours.
Zondi would not give any details, saying: "You'll get to hear the case when he appears in court".
Fellow journalists said the arrest relates to an incident to Mpumalanga, and that Wa Afrika was being taken there.
Wa Afrika recently published an article which alleged that Police Commissioner Bheki Cele had improperly purchased a new building for police headquarters at a cost of R500 million.
Referring to this, Sunday Times editor Ray Hartley said in a statement to staff:
"We have assigned lawyers to represent him and we are trying to establish what the charges against him are and where he is being held".
"Our lawyers have been unable to get a clear answer from the police on either of these two questions.
"I am deeply concerned at the fact that a journalist can be arrested and held at an undisclosed location in a country where the rule of law ought to apply."
Hartley said: "He was arrested by a large number of policemen in an operation that was clearly designed to intimidate and I can only conclude that this was the true motive for what took place today.
"Mzilikazi was one of the authors of the story which we published on Sunday about the rental of new police headquarters at the cost of R500m without following the usual tender proceedings.
"I want you to rest assured that we are doing everything in our power to have him released and that we are doing all that we can to assure his well-being."
Marvin Meintjies, the Sunday Times National News Editor, also sent out a statement pledging his support of Wa Afrika.
"The arrest of one of our colleagues on spurious charges brings into sharp relief the fight we have on our hands," Meintjies said.
"The Info Bill, the proposed media tribunal, are all aimed at closing the democratic space within which we operate - and for which we fight.
"The Sunday Times will provide all the support we can to our colleague Mzilikazi wa Afrika - and we will continue to protect our sources. No doubt with the full backing of Sanef.
"Our best defence - in fact, the only option we have in these times - is to continue to be excellent at what we do."