The players disappeared nine months after two players with the Cuba women's team fled to the United States following a match against Canada in Vancouver.
Blatter said Monday that the defections had become "a presidential question" for FIFA and not just an issue for the competitions department.
"This we cannot let just stand there — it will not work," he told reporters at a briefing.
Blatter will study FIFA's reports into the latest incident in Toronto last Thursday before acting.
The FIFA president said he will personally contact "the sports authorities in Cuba, but giving them a copy to give to their political authorities."
Cuba had just 11 players available to face Canada on Friday and lost 3-0.
Cuba was already eliminated from contention in its group, and sent an inexperienced squad to Canada — prompting suggestions that top players were left at home to prevent them defecting.
"As with any Cuban sport team that travels around the world, they're all chasing the American dream," Cuba coach Alexander Gonzalez said after the match about the missing players. "And it's difficult to try to keep the team together. Obviously it's a difficult situation for the team and it's tough for me to talk about it."
The Cuban coach said he had been working new players into his team, players with "a passion and a love of the game.''
The Canadian Soccer Association disputed that the Cuban team it beat was inferior, saying nine of the 11 Cubans were veterans of the CONCACAF Gold Cup.
Blatter, whose scheduled visit to Cuba next week was postponed earlier this month, said he plans to visit the Caribbean island in either February or March.
The FIFA president declined to be drawn into a football politics squabble between Uruguay and FIFA vice-president Jim Boyce of Northern Ireland.
Uruguay officials wrote to Blatter last week demanding he censure Boyce for singling out their forward Luis Suarez of Liverpool as a major culprit in making diving a "cancer" of the sport.
Blatter said he believed that officials "should not identify players" to make a point about potential misconduct, but it was not a significant issue.
"This declaration is a very, very small part of the problems we have to deal with in the world of football," Blatter said.