Four stadiums remain under construction, while work outside many of the venues in the 12 host cities is still ongoing and further doubts linger over the completion of airport facilities and fan parks.
Sao Paulo's Arena Corinthians, due to host the opening match between Brazil and Croatia, has been plagued by problems, including the death of two workers after a crane collapsed on the site.
The stadium in Curitiba will also not be ready until a month before the tournament.
Preparations have additionally been marred by security concerns, with protesters claiming the money spent on the showpiece event would be better used improving hospitals, schools and infrastructure.
"Listen, 100 days, it's a long way to go, and it's a short way to go if there are still problems," Blatter said.
"But now all problems are under control and it will be, in 100 days, an exceptionally good start for an exceptional competition.
"The Brazilian spirit of the game and the Brazilian ability to play football makes this World Cup very, very special. I am sure it will be a great, great success."
Several events across Brazil are set to mark the 100-day point, with host cities planning to light up traditional buildings in the colours of the Brazilian flag.
Brazil's deputy sports minister, Luis Fernandes, delivered a defiant message of his own, saying: "Eight stadiums are ready and the ninth, in Manaus, will be delivered on Sunday.
"The others will also be ready with enough time to be tested before the World Cup."