"In principle, FIFA does not support any project which does not correspond to its philosophy," football's governing body said in a statement sent to Reuters.
"In respect to the planned stadium construction in Zurich, that means that if the plans are maintained to reserve some places for standing fans, FIFA must rethink its commitment to the promised 20 million Swiss francs.
"FIFA is convinced, that all-seater stadiums guarantee more comfort and, above all, more safety. Therefore, FIFA argue for stadiums which exclusively for seated fans."
Zurich has not had a purpose-built football stadium since the Hardturm, the former home of Grasshoppers Zurich, was closed 2007.
The city government is planning to build a new stadium to open in 2017 which would have a capacity of 16,000 for international games and 19,000 for domestic games and would be used by FC Zurich and Grasshoppers.
The total cost is estimated at 150 million Swiss francs.
Both clubs currently stage matches at the Letzigrund athletics stadium, which was used as one of Switzerland's four venues when the country co-hosted Euro 2008 with Austria.
Standing fans are banned in all competitions organised by FIFA and European football's governing body UEFA, including the World Cup qualifying tournaments, Champions League and European Championships.
In England, standing areas were banned following the Hillsborough disaster in Sheffield in 1989.
However, standing areas are allowed at domestic games in Germany where many clubs have removable seats which are taken out for Bundesliga matches and put back for internationals.
Switzerland also allows standing fans but the country also has a serious hooligan problem, which many believe is to blame for the small attendances at local games.
In October, the Grasshoppers-Zurich derby was abandoned because of a crowd riot.
FIFA said that if the contribution was withdrawn, it could be used for football development programmes in Switzerland instead.
