"I won't be able to comment on that right now. There will be a press conference tomorrow in response to the article," spokesperson Patrick Craven said.
The Sowetan reported that only two of the trade union federation's members complied with the Labour Relations Act, which requires unions to submit audited financial statements, membership figures and lists of office bearers by March 31.
Of Cosatu's 20 affiliates, only the National Union of Mineworkers and the SA Society of Bank Officials had submitted all the documents.
Close to 1.7 million workers, members of the 16 unions that face deregistration, could lose their bargaining power, the newspaper reported.
The SA Democratic Nurses Union and the Communication Workers Union have already been deregistered.
Congress of SA Trade Unions spokesperson Phindile Kunene told the publication it was aware of the registrar's report pointing to non-compliance.
"This will be a big issue for debate in our congress next month," she said.
"The federation feels that the registrar has been overzealous in reaching the conclusion about non-compliance."