South African President Thabo Mbeki has urged Africans to support self-determination for Western Sahara.
South Africa's move has angered Moroccan authorities
The territory has been at the centre of a dispute since former colonial power Spain pulled out in 1975, and neighbouring Morocco invaded it.
The president's remarks follow Wednesday's decision by South Africa to open diplomatic relations with the region, which has angered Morocco.
They have recalled their ambassador to South Africa for consultations.
"It is a matter of great shame and regret to all of us that... the issue of self-determination for the people of Western Sahara remains unresolved, " said President Mbeki, speaking at the opening of the new Pan-African parliament in Midrand, South Africa.
The foreign ministry in Rabat has described the move as "surprising and inopportune".
On Wednesday, South Africa's Foreign Minister Nkosazana Dlamini-Zuma told parliament of the decision to recognise the Sahrawi Arab Democratic Republic, the authority set up by the Polisario Front, which has been fighting for independence for Western Sahara.
She hoped there would be no diplomatic repercussions as a result, but said they were left with no choice because of the slow progress of the UN peace process, Reuters reports.
James Baker, former UN special representative for Western Sahara, resigned in June following Morocco's rejection of a plan to resolve the dispute.
The UN-backed plan includes a referendum on self-determination for the Sahrawi people, but Morocco refused to accept any loss of sovereignty over the area.
New UN mediator Alvaro de Soto has said that he will pursue the same policy as his predecessor.
The UN has spent more than $600m on peacekeeping efforts in Western Sahara as it has attempted to resolve the issue over the last 13 years.