Riot police detained 60 people in the red light district, officers said.
Football Supporters' Federation chief executive Kevin Miles said that there could be "no defence of the atrocious anti-social behaviour by a minority of English fans", citing the cause of the trouble as "a significant number, particularly of younger people, who had little interest in the football, and no intention of going to the game".
Thousands of supporters travelled to Amsterdam to match the football, but there was disorder in the Dutch capital despite England winning 1-0.
Thirty five of those arrested spent the night in cells and 94 were fined, police said.
Manchester United midfielder Jesse Lingard scored England's goal.
A legion of England fans were arrested after a video has surfaced of at least 25 of them launching booze and plastic cups at a group of women in a boat, following by one of them diving into the Amsterdam canal.
There were 5,234 official England Supporters Club ticket holders in the away section at the Amsterdam Arena.More news: Famous Alumni Wish Red Raiders Luck In Sweet 16
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"Without knowing the details. obviously it's not something I want to hear because most of all for us, I think our players have represented their country really well tonight with pride and some style".
"Anything else that takes away from that performance for them would be a great shame".
The flare-ups in Amsterdam come a year after despicable scenes marred England's friendly against Germany in Dortmund.
"The behaviour of a large number of England supporters was appalling", said deputy chief constable Mark Roberts, the National Police Chiefs' Council (NPCC) head for football policing.
A total of 27 members were suspended for their behaviour in Dortmund.
"They attacked us for no reason".
Josh Mahoney, 23, is in Amsterdam with family for his first England game and told the Press Association the police were "very heavy handed". "We had been in there several hours with no trouble at all".