Some 1,000 police officers on Thursday used water cannons and pepper spray to break up a rally of about 2,000 demonstrators in the southwestern city of Stuttgart, protesting against the €4.1 billion ($5.5 billion) project, which foresees moving the city's station underground.
Police initially said 116 people were injured, but on Friday raised the toll to 130. It said 16 of the injured demonstrators had to be brought to hospitals. Six officers were also hurt, and 26 demonstrators were temporarily detained, police said.
Merkel strongly endorses the right to peaceful protests, but said the project has been democratically approved and must go forward, her spokesman Steffen Seibert said.
Protest organizers said they expect some 70,000 people out to demonstrate next to the construction site on Friday night.
Carola Eckstein, a spokeswoman for the protesters said, more than 2,000 were are already on the ground, but police put their number at several hundred.
The recent protests threaten to halt the construction of Stuttgart 21, which is one of Germany's major infrastructure projects.