South Africa's biggest labour unions on Wednesday urged workers not to participate in anti-immigrant protests that have seized the country, and said they could face consequences if they skip work to attend.

South Africa is on edge ahead of a June 30 deadline which anti-immigrant groups have given for all undocumented foreigners to leave the country. Protests and potential civil unrest are expected, after weeks of sometimes violent xenophobic attacks.

Four major unions including the Congress of South African Trade Unions (COSATU), which represents around 2-million people, said in a statement that workers would not be protected if they do not go to work on June 30.

"We urge workers to report for duty and not place their employment at risk," they said.

The unions echoed President Cyril Ramaphosa's call on Tuesday not to scapegoat migrants for South Africa's problems.

"Removing foreign nationals from workplaces, communities or public spaces will not reopen factories, repair municipalities, strengthen public healthcare or create sustainable jobs," said the unions COSATU, FEDUSA, SAFTU and NACTU.

Africa's largest economy has more job opportunities than many other African countries and has long attracted large numbers of foreign workers. Some politicians have seized on the issue in recent months to blame such migrants for widespread poverty and crime.

South African media outlets reported on Wednesday that clashes had erupted between police and thousands of Malawians awaiting repatriation in the coastal city of Durban. Police fired stun grenades and teargas after a crowd became agitated, said News24.

Malawi said earlier in the week that 10 000 of its nationals were in distress and hoping to return from South Africa. While the country has been organising buses to bring them home, it put out a public call for donations to assist with the effort.

"Government is resolute in its commitment to bring home every Malawian who wishes to return from South Africa," the government said.

"However... the scale and urgency of the operation have created unprecedented financial, logistical, and humanitarian demands."

Other countries including Ghana, Nigeria and Mozambique have also repatriated citizens due to safety concerns.