Mowaffaq al-Rubaie said he had secured Grand Ayatollah Ali al-Sistani's support during a meeting in the city of Najaf on Wednesday.
The Shia clergyman gave his assent as Iraq's government pushed ahead with a plan that will attempt to stablise Baghdad, the country's capital, by disarming Shia and Sunni militias.
US commanders and Iraq's Sunnis say that the crackdown must also include militias loyal to Shia clerics.
Güncelleme Tarihi: 20 Eylül 2018, 18:16
On Tuesday, Iraqi government forces launched an assault, later backed by US forces, against the Haifa Street area of central Baghdad in an attempt to kill Sunni fighters based there.
"His eminence al-Sistani recommended an emphasis on the implementation of the law without any discrimination based on identity or background," Rubaie, a Shia, told reporters on Wednesday.
"He also asserted the need for weapons to be in the hands only of the state, and to disarm those holding weapons illegally."
Al-Sistani hardly ever makes public statements but - as the spiritual leader of Iraq's Shias - is believed to wield considerable influence behind the scenes.
Epicentre of violence
Nuri al-Maliki, the Iraqi prime minister, announced on Saturday that he planned a major security plan to restore order in Baghdad, the epicentre of violence in Iraq.
|Iraq's government is trying to take control of Baghdad's streets [AFP]|
Asked if al-Sistani had given a green light to the Baghdad security plan, Rubaie said: "His eminence is not interfering in the details but we can say that he stressed that weapons should be only in the hands of the state."
US commanders and politicians say that Iraq's Shia-led government must attempt to silence Shia militias as well as Sunni Arab insurgents, singling out the Mehdi Army, a militia loyal to Shia cleric Moqtada al-Sadr, as a prime cause of sectarian violence.
Al-Sistani has urged Shias in the past not to employ violence, although the rise in sectarian bloodshed over the past year has highlighted the limits of his authority.
He is also the sponsor of the United Alliance bloc to which al-Sadr, al-Maliki and the other Shia political leaders belong.
Asked whether he had discussed disarming the al-Mahdi Army with al-Sistani, Rubaie declined to comment.
Al-Sistani's meeting with Rubaie comes three days after the Shia cleric met al-Sadr for the first time in over a year.
Rubaie said al-Sistani had also urged the government to help people driven from their homes by violence.