Blatter's challenger is Prince Ali bin al Hussein of Jordan, 39, who has campaigned on the need for reform at the multi-billion dollar world body which has faced a series of scandals in recent years.
The vote started at 1505 GMT and was expected to take at least one hour.
Blatter, 79, who became president in 1998, is seeking a fifth term and needs a two thirds majority of the 209 member federations to win in the first round. A simple majority is enough if the battle goes to the second round.
"I am held responsible for the storm. OK yes I accept this responsibility," he told a FIFA congress.
"I promise a strong FIFA, I want to climb back up the hill, arrange FIFA's situation. I want a beautiful FIFA, strong out of the storm," he said before voting started.
Prince Ali promised to establish "transparency" if he wins.
The Jordanian prince said he would "restore respect for the body we represent" after the corruption scandals that have hit FIFA this week.
