Zwelinzima Vavi has denied Cosatu was investigating him, but confirmed there would be "further discussions" at affiliates level.
He did not elaborate on the issues that were to be discussed.
Vavi told eNCA in an interview on Thursday morning that "insinuations" had been made at Cosatu's central executive committee meeting, but no allegations were made in categorial fashion against him. He insisted there was a disinformation campaign under way by leaders who leaked information to the press.
On Wednesday the Mail & Guardian reported Vavi was to be investigated for a number of allegations, including financial impropriety relating to the Congress of South African Trade Unions's new building.
The investigation related to the acquisition of the federation's new building, as well as the sale of the previous building.
The decision to investigate the Cosatu general secretary was taken by the central executive committee – the federation's highest decision-making body – this week.
Three senior Cosatu leaders, who attended the tense meeting, told the M&G the body resolved to establish the committee of presidents and general secretaries of affiliates be formed to determine terms of reference and appoint an independent commission of inquiry to investigate all the allegations against Vavi. They will investigate all the allegations raised during the meeting.
The move is likely to further deepen divisions within Cosatu. For sometime now, there has been serious tension between Vavi and senior Cosatu leaders, including the federation's president Sdumo Dlamini.
Unions that support Dlamini include the National Union of Mineworkers, the South African Democratic Teachers Union (Sadtu), The National Education, Health and Allied Workers' Union [Nehawu] and police union Popcru. The leaders aligned to Dlamini have accused Vavi of being too critical of the ANC, the government and President Jacob Zuma.
Cosatu leaders who attended the meeting told the M&G on Wednesday several Cosatu unions launched a scathing attack on Vavi and demanded tough action against him. The affiliates initially demanded that he be put on special leave, pending the investigation, but the committee decided not to suspend him immediately.
Another allegation against Vavi includes collaborations with opposition parties, including the newly formed Agang headed by activist and academic Mamphela Ramphele, and Cosatu's rival unions to destabilise the government and the ANC.
A Cosatu leader who attended the meeting said: "This was the toughest meeting I have ever attended. There was very strong exchange of words. Vavi was in tears. He was attacked left, right and centre. He lost words in his mouth.
"He could not even go for lunch. He started negotiating with unions when he started realising he was on his way out.
"The majority of unions were very vigilant against him. He had very little support. The only big unions that supported him was Numsa and Fawu."
Vavi was not available to comment at the time of publishing. Cosatu spokesperson Patrick Craven said he was not prepared to respond to anonymous sources.
"You have to come to our press conference tomorrow [Thursday] at 11am and ask those questions," said Craven.