"FIFA has nothing to do with politics" said Emmanuel Maradas, a FIFA spokesman and special assistant to Sepp Blatter, the organisation's president.
"Iran is a FIFA member, they have qualified for the World Cup and they will be there to play football for the good of Iranian youth and for the good of peace."
The idea of expelling Iran from the tournament in Germany was raised by European and Israeli politicians after Mahmoud Ahmadinejad, the Iranian president, described the Nazi Holocaust as a "myth" and Iran resumed disputed nuclear activities.
Iran's national squad is scheduled to play its first match against Mexico in Nuremberg on June 11. The other teams in qualifying Group D are Portugal and Angola.
Some critics have suggested that the UN Security Council should act to ban the Iranian squad from the final tournament.
"The Security Council's decisions are not a concern of FIFA," Maradas. "Iran will be welcome in Germany."
On Friday, Iran and the European Union were reported to be inching towards a compromise that would allow Tehran to run a scaled-down version of a uranium enrichment programme.
The development was significant because the Europeans and the United States have for years opposed allowing Iran any kind of enrichment capability with the potential for misuse to develop atomic weapons.
Maradas was in Jakarta at the head of a FIFA delegation taking the newly renovated World Cup trophy on a tour of 29 nations in Africa, the Americas, Asia, Australia and Europe.