Home Affairs Minister Aaron Motsoaledi said that the fugitive Bushiri couple did not slip out of the country using any of their 10 passports.
They also didn't get any help from Malawi's president, Motsoaledi's told MPs on Wednesday morning following the embarrassing escape last week of pastor Shepherd Bushiri and his wife, Mary.
"I must emphasise that Mr Bushiri has five passports. None of them is South African. They were all issued in Malawi. We've got their passport numbers. Mrs Bushiri has got five passports."
They are meant to appear in a Pretoria court on Thursday to face charges of fraud, theft and money-laundering.
The pair's bail has now been revoked and they also face losing their home in South Africa.
African National Congress (ANC) MP on the Home Affairs portfolio committee, Asnathi Molekwa, said that all government departments concerned must be investigated.
"I think it's very suspicious due to the fact that Mr Bushiri cannot just leave the country without any trace. This poses a very serious security risk in the country."