Speaking to the media, Cosatu general secretary Zwelinzima Vavi said Cosatu was worried about the lack of left-wing allies in the national executive and national working committees of the ANC.
Vavi's threat follows an SA Communist Party statement that accused "certain businessmen and politicians" of using "corruption and patronage politics" to advance their leadership ambitions in the ruling party.
"The voices of this small minority accusing us of hijacking the ANC for narrow reasons have been growing louder and louder.
"The agenda seems to agitate for a regime change and it is not clear how far they are prepared to extend the envelope," Vavi said.
He said Cosatu was prepared to defend the gains made in Polokwane, where they ousted Thabo Mbeki from the presidency.
"This war won't be won from our air-conditioned offices but in the branches and structures of the ANC, just as it happened in the build-up to Polokwane".
The relationship between the members of the alliance has been strained since President Jacob Zuma took over.
Some within the ANC have publicly accused Cosatu and the SACP of trying to take over the party.
The general secretary said the anti-left faction hadfirst targeted the ANC deputy president, Kgalema Motlanthe, "who was smeared in the media", but the focus seemed to have shifted on to the ANC secretary-general, Gwede Mantashe, and he feared that it might soon be directed at President Jacob Zuma.
On the Young Communist League's call to charge Mbeki and former health minister Manto Tshabalala-Msimang with genocide for their stance on HIV/Aids, Vavi said there was no need to pursue such actions now "as that was an unfortunate page of the past and opening it would be opening the wounds."
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