President Cyril Ramaphosa's office has denied claims that it is supporting Hamas.
It said the government has bilateral relations with the Palestinian Authority, led by Mahmoud Abbas.
The ANC has had relations with the Palestinians since it was led by Yasser Arafat.
When Arafat died, Abbas took over the Palestinian Authority.
Ramaphosa's spokesperson, Vincent Magwenya said on Tuesday that the government has no relationship with Hamas.
"Reports of the South African government offering support to Hamas are false. We do not have a bilateral relationship with Hamas. We have bilateral ties with the Palestinian Authority. Support for the Palestinian struggle against occupation does not equate to support for Hamas," said Magwenya.
Ramaphosa said on Monday, after the end of the ANC National Executive Committee meeting in Gauteng, there should be negotiations between Israel and Palestine.
He said they support a two-state solution based on the 1967 borders.
He also called for an end to the blockade of Gaza to allow aid agencies to deliver basic needs for Palestinians.
Israel has ordered 1.1 million Palestinians to be moved from the north of Gaza to the south.
But many countries said this would deepen the humanitarian crisis.