Cosatu in the Western Cape as called for the removal of provincial Education MEC Debbie Schäfer.
Cosatu said it was "shocked and highly disturbed" by the way Schäfer had handled the feeding scheme saga in the province.
Schäfer announced on Monday that the department had been allocated emergency funding to support pupils who ordinarily received meals at school during terms.
The federation said it was quite clear that Schäfer was out of touch with the realities of what was happening on the ground and lacked the leadership skills to deal with the matter.
"While the president and his government are really trying very hard to prevent Covid-19 from spreading, the MEC is doing the opposite," Cosatu said.
"We condemn her conduct in the strongest possible terms and herewith support the call by the South African Democratic Teachers' Union (Sadtu) for her immediate removal as MEC of Education in this province."
Cosatu said it can't allow children to risk being infected with Covid-19, while there are other ways and means to feed them.
Call for Schäfer to be charged, investigated
"We call on the premier of the Western Cape to remove the MEC with immediate effect and to replace her with a capable person. We also call on the national health minister to intervene in this matter," Cosatu said.
The federation also called for Schäfer to be charged for contravening the lockdown regulations and for an investigation by the Human Rights Commission.
On Thursday, Schäfer told GroundUp that Sadtu's call showed how out of touch the union was with what was happening on the ground.
"I am extremely saddened by Sadtu's response. We have had such an overwhelmingly positive response to our initiative, after weeks of requests from desperate communities, that I cannot understand how any organisation can be opposed to this," she said.
"We have issued detailed protocols to schools for the implementation of this essential work to ensure that social distancing is maintained and that our learners and staff are kept safe," Schäfer added.
One of the schools opened to feed pupils on Wednesday was Voorspoed Primary School in Hanover Park in Cape Town. Principal Reginald Esau said things went very well and more than 300 pupils were served.