In both larger metropolises on Sunday, security forces used water cannon as well as batons, horses and dogs - and in Eindhoven tear gas - to quell the protests.
Protesters had gathered in defiance of lockdown orders in at least 10 towns and cities Sunday, looting stores and clashing with police after authorities imposed a new nighttime curfew - the first in the Netherlands since World War II.
Some of the worst violence flared in Eindhoven in the south, where rioters threw stones, knives and fireworks at police and damaged the local railway station, Dutch media reported.
Eindhoven mayor John Jorritsma told reporters that if the country continued "down this path, then I think we are heading for civil war".
A far-right, anti-immigration group, Pegida, had previously called a demonstration in the city and said they would use the protest to burn copies of the Quran.
Unrest also erupted in The Hague, Breda, Arnhem, Tilburg, Appeldoorn, Venlo and Roermond.
A group of youths in the village of Urk attacked the Police with fireworks and set on fire a Covid-19 testing centre.
'The fire in a screening centre in Urk goes beyond all limits, ' Health Minister Hugo de Jonge said on Sunday.
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Police said yesterday that they had fined more than 3,600 people nationwide for breaching the curfew that ran from 9pm on Saturday until 4.30am yesterday, and arrested 25 people for breaching the curfew or for violence.
The Netherlands has also restricted global travel - banning travel overseas until March 31 - and limited flights from the United Kingdom and several South American countries.
Parliament voted narrowly last week to approve the curfew, swayed by assertions that a variant of COVID-19 first identified in Britain was about to cause a new surge in cases.
Schools and non-essential shops in the Netherlands have been shut since mid-December, following the closure of bars and restaurants two months earlier.
Dutch lawmakers on Thursday approved Rutte's curfew plan, though on condition that it begin half an hour later than the original 8:30 pm start time.
'I stand here for freedom.
Rutte and his cabinet resigned on January 22 over a scandal involving child tax benefits, but they will continue to govern until elections in mid-March.