Fikile Mbalula branded the hosts "useless" and a "bunch of losers" following their group-stage exit from the African Nations Championship, where their only victory came against Group A basement side Mozambique.
However, Zuma has come out in support of Gordon Igesund's men, made up entirely of players plying their trade for clubs in South Africa, who saw Mali and Nigeria claim the top two spots in the group.
"The fact that the team lost, that doesn't mean anything as other teams lost as well," he said.
"Some want the team disbanded. It has improved greatly and needs support."
Despite a poor showing in the tournament, which ended with a 3-1 defeat to Nigeria, Zuma feels Igesund is the right man to take the side forward.
"We're well aware that some people are criticising the way the national team played against Nigeria," he continued.
"The current coach knows what he's doing. He's great at his job."
But South African Football Association president Danny Jordaan hinted that an overhaul the country's set-up was afoot, adding: "I am fully aware that the national team needs urgent attention and we are dealing with the situation.
"We have a meeting already scheduled in early February where the team name, technical staff and technical sponsorship will be addressed."
