The power cut meant no trains to or from Amsterdam's busy main rail station, resulting in a rush of drivers onto the road and heavy traffic.
"Other parts of the country are hit by the knock-on effect," Dutch National Rail said on its website.
"The power cut has since been fixed but rail traffic is still seriously affected," it said shortly before 10:00 am.
The power cut was repaired by 0800 GMT, electricity provider Liander said, but it warned "problems may still occur due to the start-up process."
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Early Tuesday, large parts of Amsterdam and its northern neighbours Zaandam and Landsmeer were hit by the massive power cut, affecting some 360,000 households and public transport including the capital's tram service, Liander said.
Dutch road safety association ANWB warned that heavy traffic jams had formed on the A2 highway between Amsterdam and Utrecht.
Dutch public newscaster NOS meanwhile showed television images of commuters resignedly waiting for the problem to be fixed at Utrecht's central station, while long queues formed at bus stops at Amsterdam Central station.