"He was arrested by a large number of policemen in an operation which was clearly designed to intimidate and I can only conclude that this was the true motive for what took place today," said Sunday Times editor Ray Hartley in a statement.
Hartley said that Wa Afrika was one of the journalists who worked on a story that alleged police commissioner General Bheki Cele had leased new police headquarters for R500m without following the normal tendering process.
"I hope, for the sake of our country, that he was not arrested on spurious charges in order to punish him for what he wrote," he said.
Hartley said the paper had assigned Wa Afrika lawyers who were still attempting to find out what the journalist would be charged with and where he was being held.
"We are doing everything in our power to have him released and we are doing all that we can to assure his well-being," said Hartley.
He said lawyers suspect that Wa Afrika was arrested for allegedly possessing what police claim is a fraudulent letter of resignation from Mpumalanga Premier David Mabuza to President Jacob Zuma.
"They suspect that's what may be behind this," said Hartley.
Hawks spokesperson Musa Zondi confirmed that a Sunday Times journalist had been arrested for fraud and defeating the ends of justice.
"It's interesting that he should make that statement because the police refused to tell us what he was charged with," said Hartley.
Zondi said Wa Afrika would appear in court within 48 hours.
He declined to provide further details.
"You'll get to hear the case when he appears in court," said Zondi.