Images on social media show riot police shouting at demonstrators and hitting them with batons after they got off a bus on the outskirts of the city.
Hundreds of demonstrators wearing Palestinian scarves chanted slogans and gathered at De Dam square, despite the ban imposed after last week's violence when the football team Ajax hosted Israeli Maccabi Tel Aviv in Amsterdam.
The city had given permission for a protest on Wednesday, on the condition that it would be held at a location outside the city's central areas.
"These demonstrators were transported to this location after they were previously arrested at De Dam for violating the emergency ordinance", the police write in a statement.
