He cited reports of mistreatment of civilians by members of rhe federal police and the Hashed al-Shaabi (Popular Mobilisation) paramilitary forces and urged Prime Minister Haider al-Abadi to enforce discipline among government ranks.
There is "information indicating that some violations were carried out by some members of the federal police and some volunteers against civilians", his office said in a statement.
"These actions are a disservice to the sacrifices... Made by our heroic security forces," Juburi's office said.
Juburi, a Sunni politician, had warned from before the launch of operations to retake Fallujah of the risks of reprisals against the local population.
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Fallujah is a Sunni city that lies only 50 kilometres (30 miles) west of Baghdad and is one of the Islamic State group's most emblematic bastions.
The Hashed al-Shaabi is an umbrella organisation that includes Sunni tribal fighters but is dominated by powerful Tehran-backed Shiite militias.
It is nominally under Abadi's authority but some of its most powerful groups answer directly to Iran.
Abadi has also warned that any whiff of sectarian violence by anti-IS forces against the local population risked enflaming an already precarious national climate and would tarnish military victories in Fallujah.
Grand Ayatollah Ali al-Sistani, the most revered Shiite cleric in Iraq, has issued guidelines intended as a form of code of conduct for forces fighting IS and aimed at curbing abuses.