Mozambique said five of its nationals were killed in “xenophobic attacks” in South Africa at the weekend and efforts were under way on Tuesday to repatriate hundreds of others.

However, the South African police confirmed only that two Mozambicans had died in violence in the southern coastal town of Mossel Bay, the first killings to be officially linked to a wave of anti-migrant protests sweeping the country.

A South African teenager was also killed, police said, with reports that dozens of shacks were torched, some while people were inside them.

Protests against undocumented foreign nationals have been mounting in South Africa in recent weeks, leading Ghana to evacuate about 300 of its citizens last week, with Nigeria also announcing repatriation plans.

The Mozambique government’s media office said in a statement late on Monday that seven Mozambican citizens had died after violence broke out on Friday in Mossel Bay, about 380km (235 miles) east of Cape Town.

Five deaths were “a direct consequence of the xenophobic attacks and the other two as a result of a road accident, when they were travelling in a private vehicle on their way back to Mozambique”, it said. But the South African police told AFP that only two Mozambique nationals, aged 27 and 43, were killed in an informal settlement attached to Mossel Bay, both from multiple injuries from assault.

In the early hours of Sunday, police in the same area found the body of an 18-year-old South African who had been stabbed to death in unclear circumstances, they said.

Mossel Bay’s mayor, Dirk Kotzé, at the weekend voiced “deep concern and dismay at the current xenophobic attacks where people have been murdered, houses burned and families displaced”.

As the continent’s most industrialised economy, South Africa has long been a destination for legal and undocumented African workers who are accused by some fringe groups of crime and taking jobs from locals.

The national broadcaster, SABC, said tensions in Mossel Bay erupted over allegations that undocumented migrants were being employed by construction companies. About 55 shacks were torched, local media reported.

One Mozambican national, Dolinda Mabunda, told the Mossel Bay Advertiser: “We were still inside when people started burning down our house. I just took what I could and I ran.

Another migrant, Silvino Chauque, told SABC: “I will go back [home] because we are not safe.” He said he had lost all his possessions in the unrest.

The Mozambique government said 300 Mozambican nationals had returned home on Saturday. “The remaining just over 500 have since been sheltered in a safe location in the Western Cape Province, and as of … 1 June, the process of their repatriation to Mozambique is already under way,” it added.

After one citizen-led organisation demanded that undocumented foreign nationals exit South Africa by 30 June, there have been reports of vigilante groups checking the documentation of foreign nationals and forcing small businesses run by non-South Africans to close. The action has no official backing and has been criticised by the authorities.

Last month hundreds of foreign nationals from countries including the Democratic Republic of Congo, Rwanda and Somalia sought protection in the eastern port city of Durban, saying locals were going door-to-door to tell them to leave by the end of the month. Several countries including Kenya, Malawi, Lesotho and Zimbabwe have urged their citizens in South Africa to exercise caution.

South Africa has experienced repeated waves of xenophobic violence over the past decades. The latest spike comes as political parties seek support before local government elections in November.

In 2008, 62 people, including 21 South Africans, were killed in anti-immigrant riots that also displaced thousands. Further outbreaks followed in 2015 and 2016.