"Corruption has no place in sport," said Nathalie Vandystadt, a spokeswoman for the European Commission, the executive of the 28-nation EU.
"FIFA has been given enough time and chances to reform. Now it's time for change. The integrity of football is at stake.
"Millions of fans around the world have lost patience and they deserve better," she added while declining to comment on Sepp Blatter's re-election as the head of FIFA on Friday.
The EU was among many voices calling for reform after a week which saw seven FIFA officials arrested and 18 people connected to football indicted on corruption charges by the US Justice Department.
The Commission, however, declined to back calls in some quarters of Europe for a boycott of the FIFA World Cup scheduled to take place in Russia in 2018.
"This is not an option we have on the table. We will continue to monitor the developments in the FIFA investigation," she said.