Police Minister Senzo Mchunu confirmed the arrests during the memorial service for the 18 victims on Sunday, in the town of Lusikisiki, in the Eastern Cape, where the killings happened.
He added that the arrest of a fourth suspect would be announced soon.
Shockwaves erupted across South Africa when gunmen opened fire on two homes, killing fifteen women and three men. Several were shot in the head.
The victims were aged from 14 to 64 years old, according to local newspaper Dispatch Live.
Mchunu said the police are still trying to “piece together” a motive for the killings.
The attack happened when the family had gathered for a traditional ceremony.
The three suspects will appear in court on Monday to hear their charges.
This massacre has shocked South Africa, adding to calls for more police protection.
South Africa has one of the highest murder rates in the world, according to the latest figures from the United Nations Office on Drugs and Crime.
There were more than 27,000 murders in 2022 – amounting to 45 people per 100,000, out of a population of almost 60 million. By comparison, the US rate is six per 100,000.
It has also led for people to calls to end gender-based violence. South Africa also has a high femicide rate.
Deputy minister in the presidency Mmapaseka Letsike attended the memorial and said civil society, traditional leaders, government need to “raise the bar” to help end gender-based violence.
