The European Parliament voted by a clear show of hands in favour of an eight-page resolution with a series of demands to clean up the sport.
The resolution said that the parliament welcomed Blatter's decision to resign last week, but expressed "serious concern" that he might stay on for a further nine months before a new leader is appointed.
Urgent reforms to root out corruption and restore FIFA's credibility could not begin in earnest until then, it said.
"The European Parliament... therefore calls on FIFA to select, in a transparent and inclusive way, an appropriate interim leader to replace Joseph Blatter forthwith."
The parliament said that corruption within FIFA had seriously damaged the integrity of global football, with a "devastating impact" from the top level of professional soccer to amateur grassroots clubs.
It is also calling for FIFA to publish in full the report produced by former U.S. prosecutor Michael Garcia into the 2018 and 2022 World Cup bidding processes.
The parliament said it welcomed comments from the chairman of FIFA's audit and compliance committee, Domenico Scala, that Russia and Qatar could be stripped of World Cup hosting rights if evidence emerged of bribery in the bidding process.
Host countries, it said, should abide by international standards in respect of fundamental rights.
During a debate on Wednesday, British Labour MEP Neena Gill said she had little confidence that any reforms in FIFA would actually happen.
(Reporting By Philip Blenkinsop, additional reporting by Alexander Saeedy; Editing by Dominic Evans)
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