The World Cup begins on Thursday, with Iran playing their first two Group G games in Los Angeles, against New Zealand on June 15
and Belgium on June 21, and then facing Egypt in Seattle on June 26.
In a statement, the Iranian federation said it had already begun the ticket sales process for the matches but could no longer provide them to fans.
"This is despite the fact that many Iranian football fans, relying on the officially announced process, had already made the necessary plans to attend the matches," the FFIRI added in a statement.
"Depriving Iranian supporters of access to their lawful and official allocation of tickets is an action contrary to the spirit governing international competitions and the principle of equality among participating countries.
"This development raises serious questions about the interference of non-sporting and political considerations in the organisation of the world's biggest football event."
Each participating federation at the World Cup receives 8% of the tickets for each of their matches to be allocated to fans according to their own criteria.
'Principles of neutrality'
The FFIRI did not say who had made the decision to withhold the tickets but urged FIFA, soccer's governing body, to adhere to "the principles of neutrality, fairness, and established regulations" and called on it to prevent off-field issues from casting a shadow over the tournament.
FIFA did not immediately respond to a request for comment.
Iran's participation in the World Cup has been clouded by uncertainty since the U.S. and Israel launched air strikes on the Islamic Republic in late February, triggering a regional conflict.
The FFIRI negotiated to move the team's base camp from Arizona to Mexico, due to uncertainty over whether they would be granted U.S. visas and a growing feeling in Iran that the squad's presence in the U.S. should be kept to a minimum.
After weeks of uncertainty, the U.S. awarded visas to all the players last week - 10 days before their first match - but several members of staff did not receive them.
A U.S. official told Reuters on Friday that the administration had issued "the visas necessary for Iran to compete in the World Cup".
FIFA said earlier on Tuesday that Secretary General Mattias Grafstrom had held a "positive discussion" with FFIRI President Mehdi Taj after the team arrived at their tournament base.
“With the team now in Mexico, FIFA will continue dialogue and collaboration with the FFIRI to ensure the team and the delegation’s experience is a positive one," Grafstrom said in a statement.
