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"This is clearly an attempt to block the reelection of Blatter as president of FIFA and is an extremely serious breach of the principles of how international organisations work," Putin said in televised comments broadcast Thursday, accusing the United States of trying to "spread its jurisdiction to other countries".
Russia is due to host the World Cup in 2018 and Putin claimed that Blatter has previously rejected "pressure put on him with the aim of banning" the event in Russia.
Moscow and the West are locked in a standoff over the crisis in Ukraine and some hawkish US senators have called for the 2018 World Cup to be withdrawn from Russia.
Swiss authorities arrested seven FIFA officials on Wednesday as part of a US probe into allegations of vast corruption inside world football's governing body.
A separate Swiss investigation is looking into alleged wrongdoing in the allocation of the 2018 event to Russia and the 2022 championship to Qatar.
The FIFA elections - if they go ahead as planned - are to be held in Zurich on Friday, with Blatter seeking a fifth term and facing a sole challenger, Prince Ali bin al-Hussein of Jordan.
