Police were reportedly attacked with pepper spray, stones and firecrackers, and several officers sustained light injuries. They responded to the violence with batons and water cannon.
One police vehicle was also attacked. The clashes came as police tried to keep demonstrators from the two sides apart, as about 400 members of the right-wing camp waited for their rally to begin.
"The excessive violence against police officers in Dortmund has absolutely nothing to do with democratic protest against right-wing extremists," police chief Hans Schulze said.
The number of people injured has yet to be determined. Some 4,000 police officers were on patrol.
The counter-demonstration was organised in response to a march by about 700 right-wing extremists through Dortmund's Nordstadt district. Thousands of peaceful demonstrators also took to the streets around the city to protest the neo-Nazi rally.
Police were expecting about 1,000 far-right marchers, and some 10,000 counter-protesters – among them, about 4,000 demonstrators from Germany's left-wing scene that could potentially resort to violence.
Earlier in the day, several hundred leftist demonstrators tried to break through a street barricade, prompting police to use pepper spray and resulting in several injuries.
Saturday's anti-Nazi demonstration was organised by the state integration minister in North Rhine-Westphalia, Guntram Schneider.
On Saturday, Schneider described the annual influx of neo-Nazis in Dortmund – who stage a demonstration each year around World Peace Day – as unacceptable. The city has been home to a raucous right-wing scene for years.
In 2009, members of the far-right crowd ambushed a demonstration by labour unions in Dortmund to mark May 1 in Germany.