In a sermon delivered by a representative, Grand Ayatollah Ali al-Sistani urged the government to continue the reforms and swiftly go after the "big thieves of public funds."
Hours after the sermon in the holy city of Karbala, thousands rallied in Baghdad and a string of other cities to press demands for reforms, better services and an end to corruption. The rallies were the latest in a series of peaceful gatherings over the past month demanding change.
In Baghdad, hundreds of army and police cordoned off the rally, sealing off roads leading to the venue, the central Tahrir Square, as army helicopters hovered above.
The Iranian-born al-Sistani also cautioned against the reform campaign distracting authorities from the fight against the Islamic State, describing it as the "most Honourable and righteous battle because it is fought in defense of our existence and future."
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Iraqi troops, despite the assistance of US-led airstrikes, have struggled to claw back ground lost to the Islamic State in the Sunni militant group's blitz last year, and have yet to attempt to retake Iraq's second largest city, Mosul.
The IS now controls about a third of both Iraq and neighboring Syria.
The protesters, who have gathered for weeks now every Friday, are also calling for effective, anti-graft measures.