The players have been practicing with the shoes, which they received before beginning their training ahead of the World Cup.
Nike added that sanctions applicable to its business "have been in place for many years and are enforceable by law".
Team Melli' or Iran national football national team are among the first country to reach Russian Federation where the Fifa World cup is being hosted.
Nike will no longer supply the Iranian national soccer team with footwear for this month's World Cup, citing the Trump administration's decision to reimpose economic sanctions on the country.
Team Melli' is managed by Carlos Queiroz, former Manchester United assistant boss.
"They should come out and apologise because this arrogant conduct against 23 boys is absolutely ridiculous and unnecessary", 65-year-old Queiroz said.
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Opposition Leader Bill Shorten agreed the summit was a positive step forward, "even if some of the images were certainly unusual". It isn't a question of preparation, he said as an afterthought, it's a question of whether or not people want it to happen.
In May president Trump reimposed economic sanctions against Iran when the U.S. withdrew from the nuclear deal between Iran and other world powers that was signed in 2015.
On Monday Quieroz said that the decision could adversely affect his team's performance in Russian Federation.
Iran's coach, Carlos Queiroz, was surprised by the move, telling reporters: "Players get used to their sports equipment, and it's not right to change them a week before such important matches".
Members of Iran's soccer team have resorted to asking other players to loan them footwear or individually purchasing cleats, ESPN reported.
Iran's first match is on Saturday against Morocco.
It remains to be seen whether Queiroz's defiant verdict bears fruit, given any loser of Friday's crunch fixture in Saint Petersburg would be left needing to beat either Spain or Portugal to reach the last 16.