"We know there is another sport (baseball) in this country that is more important than football and this is a challenge for football," the head of world soccer's ruling body said on Monday during an official visit to Santo Domingo.
Blatter, on a week-long tour of the Caribbean and Central America, added: "One day, I don't know when, football will be recognised in this country on the same level".
Baseball is hugely popular in the Dominican Republic especially after they won the World Classic in San Francisco last month by beating neighbours Puerto Rico in the final.
FIFA has invested millions of dollars in the region and has major renovations planned for Dominican stadiums in Santo Domingo and San Cristobal.
Blatter is due to visit Haiti later on Monday and will also travel to Cuba.
His trip ends in Panama on Friday where he will attend the CONCACAF (North and Central American and Caribbean Confederation) Congress and its under-17 championship final in Panama City.