The Hawks confirmed the arrest on Friday, but did not name the couple.
The church, however, issued a statement confirming that Bushiri and his wife, Mary, were taken into custody on fraud and money laundering charges.
Brigadier Hangwani Mulaudzi said on Friday that the arrest took place at a "lavish hotel in Rustenburg".
"The Hawks’ case against the pair concerns alleged offences of fraud, money laundering and contravention of the Prevention of Organised Crime Act (POCA). The crimes were committed from 2015 in relation to Exchange Control Regulations related to foreign currency in an amount of $1,147,200 (about R15.3m).
"The couple who run several business enterprises in South Africa and abroad are expected to appear before the Pretoria Commercial Crime Court on Monday," he said.
The church statement said that, at about 7am on Friday, armed members of the police stormed the Sparkling Waters Hotel in Rustenburg.
"We were later made aware that they were members of the Hawks. They took the prophet and our mother, Prophetess Mary Bushiri, in handcuffs to Pretoria," the statement said.
"As you will remember, from last year, we have struggled with reports that our father [Bushiri] was guilty. He has been detained and is being questioned by the Hawks in Silverton, Pretoria."
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