The organisation was embroiled in a bribery scandal in 2011 when Blatter's presidential rival, Mohamed Bin Hammam, was accused of offering members of the Executive Committee cash in exchange for votes.
Bin Hammam was recently banned from the sport for life following a number of failed appeals, while CONCACAF president Jack Warner, who had been subject of a number of accusations over corruption throughout his 11-year reign, resigned and was therefore assumed not guilty of any wrongdoing.
It was the latest in a long line of accusations to be levelled at football's governing body, with some stretching back to when Joao Havelange ousted Stanley Rous as president in 1974.
But Blatter believes that such episodes will be a thing of the past now that Fifa has taken steps to clean up its act, as long as every member body under its rule plays their part.
"The congress in 2011 decided that we shall have a look at three different matters," he told Al Jazeera. "One was transparency in finances, one was to improve the organisation of the ethics committee, and the third was to have a better governance in all the organisations in football.
"We are now in the last phase of this implementation. In 2013, at the next congress, we will be at the end of this reform process. What is already done is that we have a special committee for audit and compliance, we now have a special committee for ethics that has two chambers - one investigatory and one adjudicatory - and we are at the end of some changes in statutes.
"This is the top of the pyramid, if we want it to work through the whole pyramid this must be installed at all the national associations and in the confederations.
"This must come. Fifa, with 300 million people, cannot just have one tribunal or one control system at the head. It's like in any country, you have to go to all the provinces and all the communities.
"It is done, but now it has to be applied. It is easy to control football when it is played on the field, because you have a referee, you have a time limit and you have boundaries. But outside the field of play you have no referee, you have no time limit and you have no boundaries.
"Football cannot be responsible for all the villainy that happens in the world. Now it is said: 'If something is wrong, it's football', 'If there is corruption, it's all football', 'If there is violence, it's football'. No. Because football is part of our society, and this game is so popular, we are victims of all the villainy, and we must fight against that. But it cannot just be from the top, it must come from solidarity."
Despite his confidence that he is winning the fight against corruption, the 76-year-old admitted that while Fifa has 'independent' figures sat on its disciplinary boards, Transparency International, a company that purports to be a "global coalition against corruption", refused to work with the organisation.
"We have independent chairmen on these committees," he continued. "Totally independent chairman - paid by Fifa.
"I had a long discussion with Transparency International. They had another view how to develop our ideas."