Sepp Blatter says Fifa is looking carefully at the decision to allow Egypt to play their World Cup tie against Ghana in Cairo.
Ghana's request to have the match on 19 November moved to a neutral venue on security grounds has been rejected.
This prompted the country's Sports Minister to request an urgent meeting with Fifa to discuss the issue.
There has been political and social unrest in Egypt since President Mohamed Morsi was overthrown by the military.
In his first public comments on the matter, Blatter said: "We should be very careful because they (Ghana) fear something should (might) happen."
"We are looking at this matter, there have been matches played in Egypt, international club matches, but we must be careful."
The Fifa president Sepp Blatter also revealed that he wants to get rid of World Cup qualifying play-off ties in future.
The head of the game's world governing body says play-offs are a hard way for teams to miss out on the finals.
Twenty teams, plus hosts Brazil, have qualified for next year's tournament via round-robin groups.
The remaining 11 places will be decided this month, all in two-legged play-offs.
Five matches will be played in Africa, between runners-up from the 10 second-round groups.
Four ties will be played in Europe, involving the best eight runners-up from nine groups, plus two intercontinental featuring Jordan against Uruguay and Mexico v New Zealand.
"It will be drama because you have to eliminate teams now in two matches," Blatter said in a video interview on Fifa's website.
"I think this is good for television, this is good for the spectacle of football but I think we should try to find a solution where at the end of the qualification, you are in or out, and not this play-off.
"This play-off.... it gives more intensive action, but for those teams (who are knocked out) it is a hard way to go."