South Africa has summoned the Rwandan envoy in Pretoria after a Rwandan pro-government news site reportedly called a key minister a "prostitute".
Lindiwe Sisulu, the South African international relations minister, has also been criticised on Twitter by a senior Rwandan official.
Her spokesman told the BBC the remarks were "unacceptable" and "must stop".
Ms Sisulu recently met an exiled critic of the Rwandan leader, triggering a diplomatic row between the countries.
She told a press conference last month that she had met Rwanda's former army chief, General Faustin Kayumba Nyamwasa, in Johannesburg.
She said she was "pleasantly surprised" to hear that Mr Nyamwasa, who has established an opposition party in South Africa, was willing to negotiate a reconciliation deal with his former government.
Mr Nyamwasa has been living in exile in South Africa since 2010, after falling out with Rwanda's President Paul Kagame.
Rwanda's Deputy Foreign Minister, Olivier Nduhungirehe, criticised the meeting on his Twitter account, in remarks South Africa described as offensive.
He said that if any South African official wanted to negotiate with a "convicted criminal" who was leading a "subversive movement", they were free to do so - but they should "never think" of involving Rwanda in the process.
A headline on a Rwandan pro-government news website also referred to Ms Sisulu as Mr Nyamwasa's "prostitute", a South African government source told the BBC's Milton Nkosi in Johannesburg.
The story was removed but the damage was done, our reporter adds.
Ms Sisulu's spokesman, Ndivhuwo Mabaya, said that the Rwandan envoy in Pretoria had been told that the tone of comments was unacceptable.
He said the South African High Commissioner in Kigali, George Twala, had also been recalled to Pretoria for consultations.
"It is our commitment to normalise the relations, but we can be more focused without being insulted on social media and the use of undiplomatic language," Mr Mabaya said.
In 2014, South Africa expelled three Rwandan diplomats in connection with an attack on Mr Nyamwasa's home in Johannesburg. Rwanda retaliated by ordering out six South African envoys.
Mr Nyamwasa has survived at least two assassination attempts in exile.
Four men were found guilty in 2014 by a South African court over a gun attack that left him with stomach wounds. Mr Nyamwasa described the attack as politically motivated.
Relations between South Africa and Rwanda also became strained after Rwanda's former intelligence chief, Colonel Patrick Karegeya, was murdered in a hotel suite in Johannesburg in 2014.
Shortly after the murder, Mr Kagame said: "You can't betray Rwanda and not get punished for it. Anyone, even those still alive, will reap the consequences. Anyone. It is a matter of time."