The car appeared to have caused little damage and photos from the scene showed several dents to the steel gates in front of the Chancellery.
The Volkswagen was daubed with messages written in white paint that read, "You damn child and old people murderers," and "Stop the globalization politics.”
Police took the 54-year-old male driver into custody for questioning, a spokesperson told NBC News. Police are investigating the cause of the incident and whether it was deliberate, they said in a tweet.
There were no immediate reports of casualties and it was not clear if Merkel was inside the building at the time of the incident. The driver was taken away in a wheelchair, Reuters reported.
The incident comes after attacks by Islamist militants in Paris, Nice and Vienna in recent weeks. Germany has also seen large protests against the government’s Covid-19 measures in recent weeks.
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Merkel is scheduled to discuss the country's coronavirus restrictions ahead of Christmas and New Years on Wednesday with the leaders of the German federal states.
Andy Eckardt repored from Mainz, Germany, and Rachel Elbaum reported from London.