A police spokesman said that around 200 tents were dismantled, mostly by their owners. "A few" tents were cleared by the police, the police said. Several hundred police officers were called to force the protesters away.
Police said around 33,000 protestors gathered on Saturday to protest against the railway station once again, under the motto "Enough! Final push against Stuttgart 21." Organizers said 55,000 people took part.
Stuttgart citizens have been protesting against the plans for weeks.
The plan aims to make Stuttgart part of the 1,500-kilometre (930-mile), high-speed "Magistrale for Europe" across Europe.
Engineers plan to blast 16 tunnels and cuttings into the many surrounding hills of Baden-Württemberg state, build 18 new bridges, lay 60 kilometres of new train track and create three new stations.
Stuttgart's terminus will be transformed into an underground through-station, with the side wings of the protected building, built between the wars by architect Paul Bonatz, falling victim to the wrecking ball.
The project is on course to become a major issue in state elections in Baden-Württemberg in March, where Chancellor Angela Merkel's conservatives, who support it, could lose power for the first time in half a century.
Supporters say that when the decision to go ahead was taken in 1995, a majority supported it, and that opponents are misleading people with inaccurate claims.