Philippe Close, the mayor of Brussels, urged football fans to stay away from the city centre and said authorities were doing their utmost to keep order in the streets.
Riots have broken out in several Belgian and Dutch cities after Morocco shocked Belgium by winning 2-0 during a World Cup clash in Qatar.
Police arrested about a dozen people after using water cannons and tear gas to disperse crowds in Brussels - and held eight more in the northern city of Antwerp.
Two police officials were injured in the Dutch port city of Rotterdam, where riot officers tackled a group of 500 football supporters who pelted police with fireworks and glass.
Disturbances were also reported in Amsterdam and The Hague.
In Brussels, police were forced to seal off parts of the city as they tried to disperse crowds.
Cars were pelted with bricks and steps were set on fire, while one person suffered facial injuries, according to Brussels police spokeswoman Ilse Van de Keere.
Philippe Close, the mayor of Brussels, urged football fans to stay away from the city centre and said authorities were doing their utmost to keep order in the streets.
Subway and tram traffic had to be interrupted on police orders.
"Those are not fans, they are rioters. Moroccan fans are there to celebrate," Mr Close said.
"Sad to see how a few individuals abuse a situation to run amok," said Belgian interior minister Annelies Verlinden.
The victory for the North African side was a big upset at the World Cup and was celebrated by fans with Moroccan immigrant roots in many Belgian and Dutch cities.
Morocco's Romain Saiss put the side ahead in the 73rd minute, before Zakaria Aboukhlal clinched the victory in stoppage time.
The result means Belgium are likely to need a win over Croatia in their final group match to qualify for the knockout stages.
