UN and South African investigators will conduct a joint probe of the four allegations of misconduct that took place in Kasai province and in North Kivu.
The allegations, which surfaced last week, involve a 17- year-old Congolese boy who was subjected to "physical violence" in eastern Kasai, said spokesman Stephane Dujarric.
Given the "serious concern raised by these allegations", the United Nations has asked South Africa to send a team of agents to the DR Congo within five days and that the investigation be completed within 90 days, he added.
Dujarric did not says how many troops were involved.
The military in Pretoria said in a statement that it took the allegations of "torture and assault" in a "serious light".
South Africa's military spokesman Mafi Mgobozi told AFP that the investigators would be dispatched to the DR Congo within days.
Under UN rules, it is up to troop-contributing countries to prosecute their nationals accused of crimes while serving under the UN flag, but the United Nations carries out joint investigations with the national authorities.
The United Nations has nearly 17,500 troops and police serving in the DR Congo, its biggest mission.
South Africa deployed around 1,300 soldiers as part of a UN intervention brigade trying to bring peace to the conflict-torn eastern DRC region.
In 2015 South Africa recalled home 50 of its peacekeepers for alleged "security breaches".
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