Apart from two deaths, nine people have been injured in violent protests in Zambela, Sasolburg, Free State police said on Wednesday.
Two of the injured were police offices, who were in a police Nyala (armoured vehicle) when it was attacked by protesters on Monday.
The other injured -- at least one of whom was in a critical condition --were protesters, said Colonel Motantsi Makhele.
Residents started protesting on Sunday in opposition to the proposed merger, in 2016, of the Matsimaholo municipality in Sasolburg with the Ngwathe municipality near Parys.
Co-operative Governance and Public Affairs Minister Richard Baloyi announced on Tuesday that the merger would not immediately go ahead.
Police continued to monitor the situation in the township on Wednesday.
Makhele said the situation was under control and that no violence was reported during the night.
"The only thing that remains is that some streets are still inaccessible," he said.
On Tuesday, a protester was shot dead at the Zamdela police station during a clash with protesters.
Earlier in the day, police said another protester was shot dead by a motorist after a group of protesters tried to block his way.
A Jacaranda radio journalist's car was pelted with stones and a Sapa cameraman was threatened with a knife.
Makhele said he could not confirm a report in The New Age that three people had died.
More than 200 people have been arrested for public violence during the protests, which started on Sunday.
Makhele said police investigations were continuing.
"With the high number of volumes of people arrested, there's a lot of administration to be done, and those arrested will be questioned. Only then will we know how many will be appearing in court and so forth."
He said the cases would probably be heard in the Sasolburg Magistrate's Court before the end of the week.