Colonel Leonard Hlathi said police fired rubber bullets as they tried to remove the taxis drivers had used to block several roads.
Tow trucks were used to remove them and roads were reopened.
Hlathi could not immediately provide reasons for the protest but said safety and security MEC Vusi Shongwe was meeting the parties involved to resolve the matter.
Democratic Alliance chief whip in the provincial legislature Jane Sithole said taxi associations blocked roads in a bid to get the government's attention.
Alternative routes, such as the N4 route from Kanyamazane and Malelane, had been blocked, bringing all traffic to the city to a standstill.
"While taxi drivers have a right to strike that is enshrined in the Constitution, they must do so in a manner that does not endanger the lives of ordinary citizens," Sithole said.
She alleged that feuding taxi associations fired shots.
On Monday group of taxi drivers called the G8 disrupted traffic in a bid to get their own taxi rank in Mbombela.
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