In Goias, fighting broke out among home fans while the referee halted the match on two occasions as they beat Atletico-Paranaense 3-0 to move into fifth place in the Serie A table.
"This is a joke, they're not real fans," said Walter, who refused to celebrate his 12th goal of the season in protest.
"We've managed to get into the top half of the table. But well not get into the top four with these kind of fans," he was quoted as saying on terra.com.br.
"Crowds are low as it is and the ones that do come get up to this nonsense."
Goias had been banned from hosting the game after fans used lasers against Sao Paulo players in a previous encounter but the club won a temporary injunction against the punishment.
The incident followed nasty scenes in Friday's Serie B match between Paysandu and Avai when Paysandu fans rioted after a second goal condemned them to a 2-0 defeat and almost certain relegation.
The referee abandoned the match with eight minutes remaining.
Soccer-related violence in Brazil, who host the World Cup next year, is common although most incidents take place in organised encounters outside grounds.
Fans from clubs that include Sao Paulo, Corinthians and Cruzeiro have all been guilty of fighting with several games halted or abandoned when the trouble threatened to encroach on to the pitch.
Cruzeiro remain top of the table, in spite of losing their third game in four, 2-1 to strugglers Coritiba.
The Belo Horizonte side are still nine points clear as closest challengers Gremio could only draw.