The co-ordinated hacking affected the @SeppBlatter and the @FifaWorldCup accounts, with messages suggesting the decision to award the 2022 World Cup to Qatar had been corrupted.
While the @FifaWorldCup account carried tweets suggesting Blatter was to stand down following corruption charges, the @SeppBlatter account 'responded' with messages purporting to be Blatter defending himself.
A FIFA statement said: "We can confirm that some of FIFA's twitter accounts, including the account of the FIFA President and @fifaworldcup, have been hacked today.
"We are looking at this issue at the moment.
"In the meantime, to avoid any doubt, we kindly ask you to verify and check any statements that you see on a FIFA twitter account with the FIFA Media department (firstname.lastname@example.org)."
A group called the Syrian Electronic Army claimed responsibility by signing off from both accounts.
The hacking began with a message which read: "FIFA executives held a meeting regarding the decision to host the 2022 World Cup in #Qatar.
"It was decided that the president Sepp Blatter is to step down due to corruption charges."
A message on Blatter's account then said: "So what if I took money from Qatari prince? I am the family's bread earner."
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- Sepp Blatter