The decision to seed the draw was widely criticised, with Republic of Ireland coach Giovanni Trapattoni claiming it was a way of ensuring the more powerful teams, such as France and Portugal, were given an easier chance of reaching next year's tournament in South Africa.
Blatter told Gazzetta dello Sport: "We should have announced it from the start.
"There is something in the rules, but it isn't clear. If we learn, we'll change for 2014, but in 180 minutes anything is possible.
"There are all the best teams (at the World Cup), if someone has missed out it is because they haven't deserved it."
Blatter will stand for re-election in 2011, insisting "I have not yet achieved my mission in football."
The Swiss has held his position since 1998 when he took over from Joao Havelange and despite often being controversial, is currently in his third term.
However, the 73-year-old plans to continue for some time.
"I've not finished my mission in football yet," he said.
"I need more time. I hope that in 2011 the FIFA congress once more has faith in me, otherwise I'll go back to my village.
"Football is my life."