Security forces in both cities used water cannon as well as batons, horses and dogs — and in Eindhoven tear gas — to quell the protests.
Vehicles were also set ablaze and shops plundered near Eindhoven's main railway station, reported regional broadcaster Omroep Brabant.
Dutch rail company NS urged travelers to avoid the Eindhoven station.
Defiance in Amsterdam
Police intervened on Amsterdam's central Museum Square, where hundreds of protesters gathered, reported public television broadcaster NOS — despite the pandemic rules limiting outdoor contacts to no more than two people.
Fearing a riot or a disease-spreading event, Mayor Femke Halsema had designated the square as a "high-risk zone" and gave police the power to preemptively frisk people for weapons.
Nationwide, more than 100 people were detained Sunday, police said.
And in Stein — near Maastricht close to Belgium — clashes with police occurred as they broke up an illegal party reportedly attended by 100 people.
In addition, more than 3,600 fines were handed out and 25 persons arrested on Saturday night as the Netherlands' first nighttime curfew of the pandemic came into force to rein in a more transmissible variant of the coronavirus. Alleged curfew violators were handed fines of €95 ($116) each.
Testing center set on fire
In Urk, a fishing industry city of 21,000 residents, on Saturday night, dozens of people hurled stones and fireworks at police.
On Sunday, municipal officials deplored the overnight rioting. "This is not only unacceptable but also a slap in the face, especially for the local health authority staff who do all they can at the test center to help people from Urk," they said.
Local authorities added that the curfew would be strictly enforced for the rest of the coming week.
"We now have a caretaker government and the political debate is heating up, going into elections in March. There is more restlessness and people are disappointed that things are taking very long, that the coronavirus is not going away and that the Netherlands is doing very badly with vaccines."
By mid-week, Dutch authorities had vaccinated just 100,000 people.