Sepp Blatter admitted the events of this week "unleashed a storm" ahead of the 65th FIFA congress in Zurich but appealed to delegates for unity.
Blatter, 79, who faces Prince Ali Bin Al Hussein of Jordan in the FIFA presidential election later on Friday, said there had been a question mark over the congress taking place.
Blatter addressed FIFA's 209 members hours before the vote in which he is a seeking a fifth term. He has refused calls to resign after FIFA was targeted by U.S. and Swiss authorities in separate corruption investigations.
Swiss police said a bomb threat has been made against the venue where the FIFA congress is being held.