"We regret that Secretary General Ban Ki-moon has withdrawn the invitation under pressure," Foreign Minister Mohammad Javad Zarif told reporters, ISNA news agency reported.
"It is also regretful that Mr Ban does not have the courage to provide the real reasons for the withdrawal," he said.
"This behaviour is beneath the dignity of the UN's secretary general."
After strong objections from the United States and the Syrian opposition, Ban withdrew his invitation to Iran, the Damascus regime's main regional ally, less than 24 hours after it was issued.
Iran refuses to consent to a transitional government in Syria, which was agreed at a first international Geneva gathering in June 2012 to end the brutal civil war.
Aladin Borujerdi, chief of Iran's parliamentary foreign affairs commission, blamed Washington for Tehran being struck off the invitation list.
"Iran's exclusion shows this body changes its opinion under the influence and pressure from the US," he said.
Zarif played down his country's absence from the so-called Geneva II conference, saying Tehran which had only received an invitation at the weekend was "not too keen on attending in the first place."
Tehran has staunchly supported Assad throughout the conflict that has killed more than 130,000 people since 2011, while being accused of providing military and financial support to Damascus.
Zarif's deputy, Abbas Araqchi, cast doubt on the success of the talks.
"It is clear that a comprehensive solution to the Syria issue will not be found when all influential parties are not involved in the process," Araqchi told state television.
"Everyone knows that without Iran the chances of a real solution to Syria are not that great," he said.
The United States, the other architect, along with Britain and France, insisted however that Iran first sign up to a transitional government plan.
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