The statement was issued on Tuesday after militants from the terrorist group Islamic State of Iraq and the Levant (ISIL) captured the northern Iraqi province of Nineveh.
After taking the provincial capital of Mosul and parts of Kirkuk, the al-Qaeda-linked militants captured two areas of Iraq's Salaheddin province as well.
Ayatollah Sistani urged the Iraqi government and political figures to stand united against terrorists.
A senior Iraqi Sunni figure has also issued a statement condemning the attacks on Iraqi cities by the ISIL.
Allameh Sheikh Ahmed Al-Kabisi has also issued a Fatwa (religious edict) saying it is a religious duty for all Muslims to fight the ISIL.
Iraq has witnessed an upsurge in violence over the past year, with al-Qaeda-linked militants regaining momentum in the country.