Blatter said the acrimonious power struggle in the region over a vote on a FIFA executive committee seat could have been avoided had Asia ensured its president, Mohamed Bin Hammam, did not have to fight for his place.
"His presidency was challenged, it looked like that," Blatter told news agency reporters at the Asian Football Confederation's (AFC) annual congress on Friday.
Blatter said he recognised why Bin Hammam had vowed to step down as AFC chief if defeated.
"I can understand why. If I have not the confidence of my congress for a FIFA seat, then how shall I continue to be president?
"What we have to do, and what AFC have to do, is make sure in future that all presidents of confederations are members of the FIFA executive committee in the position of vice president."
The confederations of Europe, Africa, Oceania and CONCACAF (Confederation of North, Central American and Caribbean Association Football) grant FIFA vice president status to their heads.
Asia and South America, however, require their confederation presidents to run in elections for a place on the panel of world football's top decision makers.
Friday's election had effectively become a vote on Bin Hammam's AFC leadership. He won by a slender 23 votes to 21 against Bahraini Sheikh Salman bin Ebrahim al-Khalifa, who had the backing of the Qatari's long-time rivals.
Blatter added: "Whoever is president of FIFA is better to have vice presidents as heads of confederations - it is easier to work together and it's better for the good of the game."
