"This is very sad for Brazilian football," FIFA told media Monday. "FIFA and the local organising committee condemn any form of violence and such incidents should not happen in any football stadium."
"For the 2014 FIFA World Cup a very comprehensive security concept is in place in an integrated operation between private and public security authorities to ensure the safety for fans, players and any other stakeholder involved in the event," FIFA said.
"The concept has worked very well during the FIFA Confederations Cup and is built on models used at previous FIFA World Cups."
Brazilian prosecutors have said they will investigate Sunday's incident at Arena Joinville in Santa Catarina state.
Police were not initially present due to a local law prohibiting them from providing security at "private events".
When they eventually arrived they were forced to fire rubber bullets to separate the fans.
Rising stadium violence has prompted concern among Brazilian authorities.
In October, four supporters of Serie B club America were shot after a Serie B match against Ceara near the World Cup host city of Natal.
In February, a teenager died when hit by a flare launched by a fan of Brazilian club Corinthians during a Copa Libertadores match in Bolivia.