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President Jacob Zuma has appealed to Cosatu to back down on its threat to fight in the streets if the government abolishes military unions.
Yesterday, Cosatu president S'dumo Dlamini told the federation's congress at Gallagher Estate in Midrand that "even in the previous difficult regime (of former president Thabo Mbeki) there was never an attempt to ban those unions. It should not happen during this administration".
But Zuma told the delegates: "If soldiers belong to unions, we could have a war coming and the soldiers feel the conditions are not right and they say 'we are on strike'.
"We must resolve the matter very comradely. As a commander-in-chief, I would like to be assured that when I say 'soldiers at war' when the time calls for it, they must be available."
The debate follows the ANC's national executive committee announcement on Sunday that it wanted the military to be "de-unionised".
The decision has not found favour with Cosatu, which accused the ANC of trying to replace military unions with the new National Defence Force Service Commission, established yesterday.
But Defence and Military Veterans Minister Lindiwe Sisulu said the commission had nothing to do with the recent protest at the Union Buildings.
Addressing the media in Parliament yesterday, Sisulu said she had long planned to set up a commission to investigate soldiers' grievances.
The commission includes UDM leader Bantu Holomisa, Freedom Front Plus MP Pieter Groenewald and North Gauteng high court judge Ronnie Bosielo.
Although it has been tasked with looking into soldiers' pay and benefits, military unions will not be represented on the 10-member commission. It will instead work with Parliament's portfolio committee on defence to come up with a new set of working conditions for soldiers.
But Dlamini said government should have long addressed racial inequalities in the army and that banning unions was not a solution.
"We want transformation in the defence force, not tomorrow but now. That will create conditions that will make protests and strikes unnecessary," he said.
University of Cape Town constitutional law professor Pierre de Vos told Sowetan that "one cannot address problems in the SANDF by passing legislation that bans disgruntled soldiers from raising their concerns".
"This will merely drive the problem underground," he said.