Hossein Kazemi Qomi said on X that direct follow-ups through credible sources show that the report was false.
He however noted that Iran has a right to deal with foreign nationals trying to enter Iran illegally.
Kazemi Qomi also said Iran is determined to return all illegal refugees to their country but it will do so in line with international law and in a responsible manner based on its policy of neighborliness and Islamic compassion.
Iran says it will expell two million illegal Afghan refugees by the next 5 months.
Reports say Iran is hosting 10 million Afghan refugees.