Sepp Blatter admitted the events of this week 'unleashed a storm' ahead of the FIFA Congress in Zurich but appealed to delegates for unity.
Blatter, who faces Prince Ali of Jordan in the FIFA presidential election later on Friday, said there had been a question mark over the Congress taking place.
FIFA also announced that the post-Congress press conference will take place on Saturday morning.
In his opening remarks to FIFA delegates, Blatter said: "The events of this week unleashed a storm.
"It was even questioned whether this Congress would go ahead but I am appealing for unity and team spirit to tackle the problems that have been created and to solve them.
"It will not be done in a single day, it will take some time.
"The important point today is to move ahead - and the important point is transparency. We have a problem to solve."
The meeting in Zurich was briefly disrupted by two protesters who unfurled a Palestinian flag - the Palestinian Football Association has demanded Israel be kicked out of FIFA - before they were removed by security.
Meanwhile, it has emerged that Brazil's FIFA executive committee member Marco Polo Del Nero left Switzerland ahead of the congress.
Del Nero's return to Brazil followed the arrest of Jose Maria Marin, his predecessor as Brazilian FA president.
Marin is one of seven FIFA officials who are facing extradition to the United States on corruption charges. A FIFA spokesperson confirmed the governing body had been notified of Del Nero's departure.
It means four of the 25 FIFA ExCo members may be absent from Saturday's meeting: Jeffrey Webb from Cayman Island and Eduardo Li from Costa Rica are under arrest, while England's David Gill has announced he will refuse to attend if Blatter is re-elected for a fifth term.
Source: PA
