"The second secretary at the Islamic Republic's Embassy in Baghdad was kidnapped by a group of people linked to [Iraq's] Defense Ministry, which works under U.S. control," Foreign Ministry spokesman Mohammad Ali Hosseini said.
The ministry demanded that Iraqi authorities release the diplomat, who was seized by gunmen outside a branch of Iran's Bank Melli in the Iraqi capital Tuesday.
It is the second incident involving Iranian diplomats in Iraq in the last two months.
In January, U.S. troops raided Iran's consulate in the northern Iraqi city of Arbil, seizing computers and documents and arresting five staff members.
The United States and Iraq's predominantly Sunni Muslim government accuse Iranian leaders of supporting Shiite militia and fueling violence in the country.
Tensions between Tehran and Washington are high over the U.S.-led campaign in Iraq and the country's policy in the Middle East at large, as well as over Iran's controversial nuclear program.
In response to Iran's perceived involvement in Iraq, U.S. President George W. Bush authorized American troops to kill or capture Iranian agents suspected of abetting the insurgency there.