The Cosatu said it had always encouraged and supported a stronger position regarding South Africa's relations with Israel.
"It must be made clear to everyone, particularly the Israeli Ambassador in South Africa, the SA Zionist Federation, and the [SA Jewish Board of Deputies] that South Africa's foreign policy is not accountable to them or even worse the apartheid state of Israel," Cosatu's international relations secretary Bongani Masuku said in a statement.
"It is accountable to the people of South Africa who gave an overwhelming majority to the ANC as a movement that defeated apartheid to rightfully support all other struggles against occupation, colonialism, apartheid and all forms of injustice wherever they happen."
On Friday, Maite Nkoana-Mashabane said the country's ministers did not visit Israel and that the board knew why.
"Ministers of South Africa do not visit Israel currently. Even the Jewish Board of Deputies that we engage with here, they know why our ministers are not going to Israel," she said at a Cosatu international relations committee meeting.
She said South Africa had not been asked to "close down" diplomatic relations with Israel, but that an agreement had been made to slow down and curtail leadership contact until things began to look better.
"The struggle of the people of Palestine is our struggle," Nkoana-Mashabane said.
"The last time I saw a map of Palestine, I couldn't go to sleep... It is just dots, smaller than those of the homelands, and that broke my heart."
The SA Jewish Board of Deputies said her comments contradicted previous assurances the minister had given to the Jewish leadership that government wished to play a role in helping Israelis and Palestinians to resolve their differences.
The YCLSA said all relations with Israel should be "terminated altogether".
"South Africans, in their numbers, are anti the policies of discrimination and racism practised by Israel against the indigenous Palestinians, and, increasingly, practised by Israel against Africans," spokesperson Khaya Xaba said in a statement.
"However, our position against Israel does not make us anti-Jewish."