Iranian Deputy Foreign Minister for Arab and African Affairs Hossein Amir Abdollahian dismissed the claim made by foreign media on Wednesday.
Earlier in the day, Al Jazeera said a round of secret talks was being held between representatives from Iran, the Syrian government and the opposition in the Swiss capital, Bern.
On January 22, the Geneva II conference on Syria, which is aimed at finding a political solution to the crisis in the country, kicked off in the Swiss town of Montreux and resumed after a one-day break in Geneva.
On January 19, UN Secretary-General Ban Ki-moon said Tehran had been invited to the Geneva II conference, but later retracted the invitation under pressure from the United States, Saudi Arabia and the foreign-backed Syrian opposition.
UN-Arab League Special Envoy to Syria Lakhdar Brahimi on Wednesday acknowledged a “quite large” gap between rival sides in the conference, and that he did not expect the talks to achieve anything substantive.
The opposition and its Western supporters, including the US, insist that President Bashar al-Assad must step down and a transitional government be formed in Syria, but Damascus has rejected the demand, arguing that the foreign-backed coalition does not represent the Syrian opposition.
Syria has been the scene of deadly unrest since March 2011. According to figures released by the United Nations, more than 100,000 people have so far been killed and millions displaced due to the violence.