The violence related to a taxi strike in Mthatha, Eastern Cape, resulted in the Electoral Commission of South Africa (IEC) being unable to operate at more than 100 voting stations.
An IEC truck was also looted when some roads were blockaded.
Police said the situation in town remained tense with many roads coming into and out of Mthatha closed on Monday morning.
By afternoon, a police deployment had to be reinforced by the sending of members of the SANDF, confirmed by Police Minister Bheki Cele.
In another incident related to the unrest, police spokesperson Priscilla Naidu said two people were wounded when they were engaged in a shoot-out with the police.
“It is alleged that at about 9am, police were following a Toyota Fortuner with five occupants on the bypass from the Ultra City joining the Ngcobo Road when shots were fired at the police members.
“Police retaliated and two suspects were injured (one in the arm and the other in the leg). Three other suspects were arrested.
“Two firearms (were) confiscated. The members involved were Public Order Policing and Mthatha Vispol members. A case of attempted murder and possession of firearms will be opened,” she said.
It was also reported that the violence led to the closure of some schools and hospitals.
The provincial Health Department confirmed that Nelson Mandela Academic Hospital, Mthatha Regional and St Barnabas Hospital staff, who worked the night shift, could not go home, while those who were supposed to report for duty could not get to work because of the blocked roads.
IEC deputy chief electoral officer Masego Sheburi said, while they had a good start to special votes, they were not able to operate due to external factors in 107 voting stations.
“The majority are in the OR Tambo region owing to the taxi strike in that area,” he said.
Sheburi said NatJoints was dealing with the matter.
“On our part we will do everything humanly possible to extend the right to vote to those people without placing at risk our own staff.”
More than 230 000 voters, who were approved for special votes by the IEC, cast their ballots in more than 22 000 voting stations across the country on Monday.
Sheburi noted that the challenges were incomparable to the number of voting stations.
“However unfortunate the reports are, the difficulties are insignificant in the greater scheme of challenge we have to undertake,” he said, adding that the challenges experienced were less than 0.1%. These also included an electoral official who was involved in an accident that resulted in the delay of opening 11 voting stations in one ward at Umuzi-wabantu Municipality.
Bosa also reported that 12 of its activists were injured and rushed to hospital after being involved in an accident en route to voting stations in Thaba Nchu in the Free State.
Sheburi said people who have applied for special votes have until 5pm on Tuesday to cast their ballots.
“If for whatever reason a person cannot avail themselves, they can come to the voting stations on May 29 between 7am and 9pm.”
Sheburi said the special votes cast will not be counted, but would be safely kept for counting with the rest of the ballots on May 29.
“We wish to reiterate that counting will take place at voting stations in the presence of party agents. No ballot will leave a voting station uncounted,” he said.
Political parties will have until Friday at 9pm to raise objections that were material to the outcome of the elections, Sheburi said.
Meanwhile, leaders of parties used the first day of special votes to cast their ballots in the Western Cape and also engaged in last-minute campaigning.
Rise Mzansi Western Cape premier candidate Axolile Notywala said his party did not receive complaints about the special votes.
Notywala said his party encouraged voters in Philippi and Bonteheuwel to come out in their numbers to vote.
“We will be at Mitchells Plain and Khayelitsha on Tuesday (today) to make sure that they turn out as much as possible,” he said.
ANC provincial chairperson Vuyiso Tyhalisisu, who cast his ballot at Spurwing Primary School in Eerste River, said that he voted to end white minority rule in the Western Cape.
“I encourage all our people to vote the DA from power,” Tyhalisisu said. DA federal chairperson Helen Zille cast her ballot at Pinelands High School.
Zille said the May 29 elections were the most important elections since 1994.
“It is going to be the first time the ANC will fall under 50% and they will never get above 50% again,” she said.
DA provincial premier candidate, Alan Winde said: “I have personally been inspired by so many of our residents who are making every effort to get to the voting station today to keep the Western Cape DA.”
EFF MPL Wandile Kasibe said: “My vote for the EFF means an end to landlessness, an end to load shedding, an end to joblessness, an end to poor service delivery and above all it means economic freedom.”
* Additional reporting Chevon Booysen and Okuhle Hlati
Cape Times