Blatter, who resigned last week despite being re-elected as head of football's world governing body, which has been consumed by an ever-widening corruption probe, intends to continue in office until a successor is designated, probably by the end of the year.
"FIFA is perplexed by the European Parliament's resolution," a FIFA spokesman said.
"As is well known, following his re-election, the FIFA President already decided, owing to the special circumstances in which FIFA finds itself, to lay down his mandate at an extraordinary elective Congress."
In a show of hands, members of parliament overwhelmingly voted for the resolution in Strasbourg, France.
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The FIFA spokesman added: "The President is focused on ensuring that at this Congress, which he is demanding, imperative reforms are passed and a new President elected."
The date for that congress will be set at an executive committee meeting in Zurich on July 20.
Meanwhile, FIFA director of communications and public affairs Walter De Gregorio resigned from his position with immediate effect.
De Gregorio, who FIFA said will continue to serve "on a consultancy basis" until the end of the year, had been in the position since 2011 and was present when Blatter announced his resignation on June 2.