JAKARTA—FIFA isn’t the only soccer organization in turmoil. Indonesia has been banned from playing international soccer, including World Cup qualifiers, and local fans are livid.

In the midst of a global scandal over alleged corruption in soccer, FIFA on Wednesday suspended Indonesia because it said the government had effectively taken over soccer activities in the country. FIFA’s statutes require that member associations be run “with no influence from third parties.” The Indonesian government has been at loggerheads with...