Police doused students with a water cannon at Amsterdam's Museum Square and charged on horseback into the crowd of about 1,000 after students pelted them with rocks, apples and bottles. Police said 15 people were arrested and two officers suffered minor injuries.
Television footage showed students throwing eggs at the entrance to the parliament building in The Hague and at the headquarters of NOS, the national broadcaster, in Hilversum.
The unrest was in response to an annual increase of 26 hours in the classroom, which the Education Ministry said was needed to raise standards and help students "master lessons."
Students argue that the schools were merely forcing them to spend more time in "study halls" to do homework, but no teaching takes place.
"There's no oversight it's complete nonsense" Kyra Esperbe, 16, told a reporter at the Amsterdam demonstration.
Prime Minister Jan Peter Balkenende criticized the students after the first protests Friday. "As a student, you can draw attention to the quality of lessons, but what has happened is wrong," he said.
Parliament is due to debate education policy Wednesday.
Students spread word to join protests on Friday and Monday using online and mobile phone text messages.
During the Amsterdam melee, students toppled a small car, then set fire to gasoline leaking from it. Others knocked over bicycles or hurled them at police, and exploded large firecrackers.
One student was arrested and put into a police van, but others grabbed his coat and pulled him out. Plainclothes officers dragged him back to the van by his hair, and arrested several others.