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Prime Minister Haider al-Abadi thanked Iraq's top Shia cleric on Friday, for his role in the war against militants, crediting him with saving the country and setting the stage for victory, despite a complicated legacy left by Shia militias.

Abadi issued a statement expressing his "deep thanks and gratitude" to Grand Ayatollah Ali al-Sistani, who called on Iraqis to volunteer to fight the militants days after Mosul fell to the Islamic State in 2014 - a step that helped to halt their sweeping offensive.

The cleric's 2014 call for volunteers "saved Iraq and paved the way for victory" over IS, Abadi said

Abadi's message comes as the battle to retake second city Mosul nears its conclusion - a redemption for forces that performed poorly there three years before.

Sistani made the call via a representative speaking at Friday prayers on June 13, 2014, days after multiple Iraqi divisions collapsed in the face of the IS assault in the north.

"Citizens who are able to bear arms and fight terrorists, defending their country and their people and their holy places, should volunteer and join the security forces to achieve this holy purpose," he said.

It sparked a flood of volunteers who were organised under what became known as the Hashed al-Shaabi, or Popular Mobilisation forces - an umbrella group for pro-government paramilitaries that is officially under the command of the country's premier.

But the call also leaves a complicated legacy, leading to a resurgence of Shia militias that have been accused of carrying out abuses, and the establishment of new paramilitary groups, both of which could be a source of future instability.

Pre-existing Shiite militias that took part in the brutal Sunni-Shiite sectarian bloodshed that plagued Iraq in past years were also placed under the Hashed al-Shaabi banner and have played a major role in operations against IS.

These groups provided a pool of capable fighters that Baghdad could rely on to combat IS.

But they have also been accused of carrying out abuses including kidnappings and summary executions in Sunni Arab areas that ultimately undermine Iraq's efforts to counter the militants.

The Hashed al-Shaabi's role after the war against IS ends, remains a key question.

Rivalries could lead to violence between units, and Hashed fighters have already clashed with Iraqi Kurdish forces in the country's north.

The Hashed may also have a political impact, with some commanders potentially seeking to translate military success into political capital in the 2018 parliamentary elections.