Pretoria - South Africa on Thursday announced that it was recalling its Ambassador to Rwanda for consultations over the issues in that country.
International Relations and Co-operation Director General Ayanda Ntsaluba confirmed that its ambassador Gladstone Dumisani Gwadiso has been recalled.
Ntsaluba stressed that the recall must not be seen as an intention to break the relations between the two countries.
"This will not affect ties between the two countries. We have no intention of expelling the Rwanda ambassador or cutting ties with Israel," Ntsaluba told a media briefing.
Relations between the two countries turned sour following the shooting of Rwandan army chief of staff, General Faustin Kayumba Nyamwasa, in Johannesburg, that drew media attention. Nyamwasa is seeking asylum in the country. The media then misquoted South Africa as saying the Rwandan government was involved in the shooting - which raised temperatures.
To address the tension, Ntsaluba said they were in consultations with the Rwandan government to find common ground and to better understand the situation.
The consultations will see how they can work better on their relations, said Ntsaluba, adding that the presence of some of Rwandan officials has had an impact on the relations.
"We are not making any connections by recalling our ambassador ...we are also not making any connection between the government of Rwanda and the shooting of the general."
Ntsaluba did not want to divulge the situation on the ground in that country, saying that the government was waiting for Gwadiso to give a clear indication of what is happening.
Rwanda heads to the polls on 9 August for the second time since the 1994 genocide.
Opponents and civil rights groups have criticised President Paul Kagame for tightening the noose on any dissident voice ahead of the election, including the media, but the authorities have dismissed the accusations as unfounded and the result of a smear campaign.