Foreign minister Sergei Lavrov also took a rare shot at UN Secretary General Ban Ki-moon, accusing him of using "crafty" language to explain his sudden decision.
"Of course this is a mistake", Lavrov told reporters in an annual briefing.
"The absence of Iran will not facilitate efforts to ensure the unity of the Muslim world, including in the fight against terror", said Lavrov.
Russia's top diplomat added that Iran, which said it would only attend the conference without preconditions, was being put into a corner by implicitly accepting the need to the regime change of its allied Syrian government.
"In essence, Iran is being asked to agree to go to Geneva to start talks about regime change", Lavrov said.
"When the UN secretary general secretary said that he was forced to rescind Iran's invitation because Iran did not share the principles spelt out in the Geneva Communique, this, in my opinion, was a fairly crafty phrase."
Ban withdrew the invitation to Iran less than 24 hours after it was issued despite reservations from the United States and Syrian opposition groups.
At the same time, Lavrov appeared to play down the significance of Iran's absence at Wednesday's discussion between regional and world powers, which precede the first direct talks between the Syrian regime and the opposition, which are planned for Friday.
"No disaster has happened", said Lavrov.
"In any case, we are talking about a one-day event on 22 January to which some 40 foreign ministers of various states including from the most remote regions have been invited."
"Of course, despite the largely ceremonial nature of this event, Iran's absence from a list of 40 states cannot but cause questions."
"The symbolism is still important", he added.
"I am just sorry that this whole story did not boost the authority of the United Nations."