The South African government says it has evidence that Rwandan diplomats were involved in cases of murder and attempted murder on South African territory.
"I [can't] lay out the progress that our law enforcement agencies are making. I am appealing to all of us to remain calm and allow them [law enforcement agencies] to do their work and allow the full investigations to be completed unhindered," International Relations and Cooperation Minister Maite Nkoana-Mashabane said on Tuesday.
Speaking at a post-State of the Nation Address briefing in Pretoria, Minister Nkoana-Mashabane said once the investigations are concluded, the country's law enforcement agencies will act "decisively and unemotionally".
She said South Africa was guided by the international law in how it relates to countries of the world, and would not tolerate any acts of criminality emanating from anyone.
"We have the rights and responsibilities as a state to provide security to all South African citizens and visitors, irrespective of where they come from. South Africa will not tolerate any acts of criminality or lawlessness emanating from anyone from anywhere in the world."
If there is a political challenge arising, the minister said South Africa would take action based on the bilateral mechanisms in place, including the Vienna Convention, which defines a framework for diplomatic relations between independent countries.
The minister's comments come after Pretoria expelled four diplomats from Rwanda and one from Burundi regarding attacks on South African soil. In response, Rwanda ordered six South African envoys out of that country.
According to a statement from the Department of International Relations at the weekend, in June 2010, there was an attack on the life of General Kayumba Nyamwasa, an asylum seeker and former Rwanda Army General. There was another attack on General Nyamwasa on 4 March. There was also an incident that led to the murder of the former Rwanda Intelligence Chief, Colonel Patrick Karegyeya, on 31 December 2013.
Rwanda has since accused South Africa of harbouring terrorists.
Minister Nkoana-Mashabane said the decision by the South African government was unemotional and government had informed the Rwandan government, in accordance with the norms informed by the country's Xonstitution and international law of conduct.
Progress in South Sudan
Meanwhile, with regards to South Sudan, Minister Nkoana-Mashabane said progress was being made in the negotiations between Sudan and South Sudan on the outstanding issues following the secession of hostilities.
Last week, South Africa's Envoy Cyril Ramaphosa visited that country to work with the people of South Sudan on reconciliation and other political matters.
Ramaphosa, who has experience in peace making efforts, will now report to President Jacob Zuma about his visit.
Fighting started in the world's youngest country in December last year when President Salva Kiir accused his then Vice President Riek Machar of mounting a coup.
Thousands of people are believed to have been killed and some 870 000 others have fled their homes - 145 000 of them to neighbouring countries and 75 000 to United Nations bases within that country, according to the UN.
With regards to Western Sahara, Minister Nkoana-Mashabane said it remained an important challenge for the African Union and for peace and stability in the region.
"Accordingly, we deemed it necessary, in the spirit of the outcomes of the African Union Summit, to take our sisterly relations with the Saharawi Arab Democratic Republic to a higher level by signing the MoU on Bilateral Consultations."
Switching focus to the Middle East, the minister said South Africa recognised the inalienable right of the Palestinian people to national self-determination in a sovereign Palestinian State, existing side by side with the State of Israel, both of which would exist within secure borders.
The minister also used the opportunity to reiterate South Africa's call for the reform of the UN and the world governance bodies who, for the past 70, remained unchanged.
"It is a well-known fact that more than two-thirds of the UN Security Council's agenda focuses on African issues. It remains a matter of serious concern that close to 70 years of its existence, the UN Security Council still remains undemocratic, unrepresentative and unfair to developing nations and small states.
"It is for this reason that I called on the UN members to set ourselves the target to celebrate the 70th Anniversary of the United Nations in 2015, with a reformed, more inclusive, democratic and representative UN Security Council," said Minister Nkoana-Mashabane.