Head of Iran's Physical Education Organization Ali Saeedlou called the ban by FIFA "illegal" and based on political reasons.
The prohibition was issued on Friday over the Iranian football players' observation of the Islamic dress code.
It prevented the Iranian squad from playing against Jordan in the second round of the qualifiers for the 2012 London Olympic Games in the Jordanian capital of Amman.
Jordan was announced to have won 3-0 following the verdict.
Islamic guidelines require women to cover their hair in public, however, FIFA women's association requires the neck and ears to remain uncovered.
"FIFA authorities had already invited Iran to the qualifiers in an official letter and this is while they were aware of the team's criteria and conditions," Saeedlou said on Wednesday.
"FIFA had previously approved of Iran women's national football team's conditions and the team had already played three games and moved to the second round," he added.
"In a letter to FIFA, we have announced our complaint about the illegal treatment of Iran women's national football team."
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