Abbas Mousavi, the ministry's spokesman, extended Iran's deepest sympathy to the government and people of Iraq, especially the families of the victims, IRNA reported.
A bomb blast occurred at Baghdad's Imam Mahdi al-Muntadhar Mosque during Friday prayers, killing at least seven people and wounding 20 others.
Police sources said the death toll was expected to rise with many of those wounded in serious conditions, according to Financial Tribune.
Either a suicide belt or improvised explosive device had been used in the attack, according to a senior police source.
There was no immediate claim of responsibility.
The incident happened after a rare period of relative calm in Iraq that had seen decades of back-to-back conflict since the United States' invasion and toppling of Saddam Hussein in 2003.