Chairman of the Investigatory Chamber of the FIFA Ethics Committee Michael Garcia stood down earlier this month following a dispute over the findings of his investigation into the bidding process for the next two World Cups, to be held in Russia and Qatar respectively.
The saga has led to calls for reform at football's global governing body, and Blatter says changes are already being made.
"This reform process is now in the face of application, implementation towards the national associations and confederations," he said. "It will take some time to go through, but it will be well done.
"The major problem we are facing with the national associations and with the confederations is the Ethics Committee, because I think sometimes people do not understand what it means to have an ethics committee, but the control and the compliance committee, discipline committee, board of appeal and the statues of FIFA, all that is going well.
"There is a lot of discipline and respect inside the 209 national associations and I can say at the next congress in May, I can be proud of the realisations in these reform processes."
FIFA announced earlier this week that it would now publish Garcia's report - a move Batter backs as he bids to regain public trust and win a fifth term in office.
"Yes, we will support the publication of the report, but in the adequate form and always and when all investigation matters are closed," he added.
"Public opinion is important because football is the greatest game in the world, connecting people, giving emotions and passion and hope, so it's very important for me at the home of football to restore the credibility and bring in the new year a good attitude for the upcoming competitions."