Sepp Blatter yesterday secured an emphatic victory over the Cameroonian candidate Issa Hayatou in the presidential election and then vowed to change the way FIFA is run over the next 100 days.

Despite months of negative publicity and a counter campaign orchestrated by UEFA and other influential FIFA officials, Blatter defeated Hayatou by 139 votes to 56, with the margin of victory catching football administrators in Seoul by surprise.

An emphatic Blatter said after the election that he will change the way FIFA is structured, by examining the possibility of turning it from an association into a commercial company.

Blatter's supporters say that doing so would make FIFA more transparent and allow it to generate more revenue. His opponents, clearly subdued after the ballot, claim that to do so will only give him more power. Blatter would have the right to appoint a board of directors which could act as an inner cabinet and bypass FIFA's executive committee, currently the bane of Blatter's life.

Blatter would then, in theory, be less accountable to the organisation he runs. Blatter claims he will also examine changing statutes in an attempt to widen FIFA's membership base. Much of his power is due to the backing of the smaller nations, whose cause he has championed during his four years in office.

The FIFA general-secretary Michel Zen-Ruffinen, who announced the election result, is likely to be removed after the World Cup is over. Zen-Ruffinen has publicly criticised Blatter over the past few weeks, accusing him of corruption, and lined himself up with the Hayatou camp.

"He [Zen Ruffinen] is in trouble," Blatter said. "If you get attacked from outside your house then it's easier to defend yourself. But if you get attacks from inside your house then you don't know how to defend yourself, especially if you don't expect such attacks. It was very sad for me but it's over."

Blatter, who hugged his granddaughter on stage moments after his victory, said: "Give me 100 days to examine how I can initiate structural changes within FIFA. We can't work with the present structure that's based on FIFA being an association; we must have a commercial structure because of our big turnover. I want to set up a commercial company that will have the mechanisms of control over FIFA."

Referring to the election campaign of the past few weeks, one of the most acrimonious ever in international sports politics, Blatter said: "The past few months have not hurt me physically but in my heart. If you ask me what I will do better over the next four years, I would say that I should avoid certain things and people. Perhaps I was too confident before; I shall now be a little more prudent in the choice of people I have to work directly with.

"I want to restore peace, harmony and unity to FIFA. I have been given a clear mandate to do this. The past few months have not been easy. I have not even had time to campaign because I have been too busy defending myself against the accusations that were made against me. It was a bitter campaign but that wasn't down to me, I was too busy defending myself."

The war of words between FIFA and UEFA is likely to calm down after Lennart Johansson, the UEFA president who has been spearheading the campaign against Blatter, conceded defeat. The row has been devastating for FIFA's reputation and has cast many of its officials in a bad light.

Johansson said he would ask his peers in the European governing body if they wanted him to resign.

"I'm not very happy," Johansson said afterwards. "Blatter has won, he's asked for co-operation and we offer him co-operation. The fight is over; we must come together for the good of football."

Johansson also hinted he would be happy to see a legal investigation into allegations of corruption against Blatter, which is being conducted by a Swiss magistrate, come to an end. He said: "If the allegation is withdrawn then I am happy to see that happen. We now want peace. I am surprised at the margin of victory but there are always winners and losers."

Earlier Adam Crozier, the chief executive of the English Football Association, had made an impassioned speech against Blatter. "Realistically FIFA has lost £215 million over the last four years. Realistically FIFA has negative equity of £ 200 million," he said. "One thing is certain, it is not good news and it will get worse."

Chuck Blazer, a Blatter ally who represents CONCACAF and also a member of FIFA's executive committee, said: "The outcome of this election has shown that dirty politics does not work within FIFA. I don't think people will make the same mistake again.

"The rifts will be remembered, it's like having a scar, you know it's there and there are some things that we can never forget. The time has now come to ensure that only those who are working for the good of FIFA are in influential positions within the organisation."

The margin of Blatter's victory has proved once and for all that he remains popular among most of the 204 national associations which make up FIFA and that despite the allegations, he is credited as spreading football's message around the world and improving facilities for many poor countries through projects he has set up.