Football's governing body says it prefers the games be played at cities closer to Olympic centre Rio de Janeiro.
FIFA says it does "not consider Manaus as a suitable first option for a hosting venue."
The statement on Friday came a day after Rio organizers announced they were adding Manaus to the list of proposed host cities to "integrate all of Brazil" in the games. The city is about 3,000 kilometres (1,800 miles) from Rio.
The other proposed cities, beside Rio, are Sao Paulo, Belo Horizonte, Salvador and Brasilia.
FIFA said the organizers' proposal will be discussed in March, when FIFA's Olympic organizing committee meets in Zurich.