"Such statements, wherever they come from, contradict the truth and are totally unacceptable," ministry spokesman Andrei Nesterenko said in the statement.
"Attempts to rewrite history, especially as the 70th anniversary of the start of World War II is being marked this year, are an offence to the memory of all victims and all those who fought fascism," he added.
Nesterenko said Ahmadinejad's comment "does not contribute to creating an international atmosphere that would foster a fruitful dialogue on issues concerning Iran."
Ahmadinejad made the statement as he addressed the annual Quds Day rally in Tehran on Friday, reiterating earlier comments that had sparked outrage around the world.
The United States, Britain, France and Germany all issued statements slamming his latest outburst dismissing the killing of some six million Jews of occupied Europe by the Nazis during World War II.
"The very existence of this regime is an insult to the dignity of the people Ahmadinejad said of Israel.
"They (the Western powers) launched the myth of the Holocaust. They lied, they put on a show and then they support the Jews.
"If as you claim the Holocaust is true, why can a study not be allowed?" he said to chants of "Death to Israel" from the crowd gathered for the annual display of solidarity with the Palestinians.
Washington condemned Ahmadinejad's comments as ignorant and hateful.
British Foreign Secretary David Miliband branded the comments "abhorrent as well as ignorant," and said they were "not worthy of the leader of Iran."
"The coincidence of today's comments with the start of Jewish New Year only adds to the insult," he added.
French foreign ministry spokesman Bernard Valero called the remarks "unacceptable and shocking. We resolutely condemn them."
In Berlin German Foreign Minister Frank-Walter Steinmeier said they shamed Iran.