Images on local media showed Ajax fans grabbing bicycles and barriers and marching towards the police HQ in the Dutch capital before officers intervened to restore order.
"The situation is unstable at the police HQ in Amsterdam. Ajax fans are vandalising the building and police vehicles," Amsterdam police said in a statement on X.
"Despite several warnings, a group continues to seek confrontation. The mobile unit (elite riot police) is now carrying out charges to drive them away," police added.
Fans had gathered earlier Sunday to protest that three of their matches had now coincided with police strikes over pensions.
Authorities ruled the 'Klassieker' match between Ajax and Feyenoord should not go ahead without a police presence. Sunday's match against Utrecht was also postponed.
Another match, away at NAC Breda, did go ahead despite police being absent due to the strike.
The F-side supporters' group said fans were "completely fed up that Ajax games are continuously the target of this sort of police action".
Ajax are furious they are already three matches behind in the championship and games have to be replayed at inconvenient times.
The Dutch giants are seeking to bounce back from last year's horror season that at one point saw them propping up the Eredivisie table.
Their two matches so far have resulted in one win and one loss.
Police have denied Ajax is being deliberately targeted. Officers were also on strike on Saturday during a major climate demo in The Hague.
