The tournament begins on November 20, with Ghana facing Portugal, South Korea, and Uruguay in the group stage.
Host Qatar has been criticised for its stance on same-sex relationships, its human rights record and its treatment of migrant workers.
The letter urges that football should not be “dragged” into ideological or political “battles” and it should not be “handing out moral lessons”.
Peaceful protests have been planned by some players.
England’s Harry Kane and nine other captains of European teams will be wearing ‘One Love’ armbands.
Denmark will wear “toned-down” shirts to protest against Qatar, with kit provider Hummel saying it “does not wish to be visible” in a tournament it claims “has cost thousands of lives”.
Australia’s squad have released a video urging Qatar to abolish its laws on same-sex relationships.
Paris, and other French cities, are refusing to screen matches in public areas, despite France being the defending champions.
The letter, signed by Fifa president Gianni Infantino and secretary general Fatma Samoura and seen by the BBC, reads: “We know football does not live in a vacuum and we are equally aware that there are many challenges and difficulties of a political nature all around the world.
“But please do not allow football to be dragged into every ideological or political battle that exists.
It adds: “At Fifa, we try to respect all opinions and beliefs, without handing out moral lessons to the rest of the world. No one people or culture or nation is “better” than any other. This principle is the very foundation stone of mutual respect and non-discrimination.
“And this is also one of the core values of football. So, please let’s all remember that and let football take centre stage.
“We have the unique occasion and opportunity to welcome and embrace everyone, regardless of origin, background, religion, gender, sexual orientation or nationality.”