Despite the recapture of swathes of territory from the Islamic State group, the conflicts in Iraq and Syria are far from over as their governments face major political challenges, experts warn.

In July the jihadists lost control of Iraq's second city Mosul in a major setback three years after declaring a "caliphate" straddling the two countries.

Across the border around half of IS's de facto Syrian capital Raqa has been retaken by US-backed fighters.

But divisions across political, religious and ethnic lines will again rise to the surface in Iraq after the extremist group is driven out of its last bastions, said Mathieu Guidere, an expert on jihadist organisations.

A month before Iraq declared the liberation of Mosul, the country's autonomous Kurdish region announced plans to proceed with a referendum on statehood in September.

The idea was not new but its timing was criticised by Baghdad, which opposes Kurdish independence, and by Washington, coming as it did with the anti-IS campaign still unfinished.

Analysts said the referendum is one of the many challenges facing the Iraq government along with the presence of a Shiite paramilitary force in Sunni-majority areas and the fate of minorities such as the Yazidis.

How the government deals with these thorny issues will determine whether it succeeds in a post-IS era, experts said.

The jihadist group "is the illustration -- violent, long and complex -- of the dystrophy that reigns in Iraq", said Mohammad-Mahmoud Ould Mohamedou, professor of international history at Geneva's Graduate Institue.

- New Iraq 'covenant' -

Ould Mohamedou advocates a "new national covenant" for Iraq that would allow the Shiite-dominated government to gain the trust of the Sunni population and other minorities, particularly in the northern Mosul region.

At the same time the government will also have to skilfully deal with the paramilitary Hashed al-Shaabi umbrella organisation which is dominated by Iran-backed Shiite militias.

Some of the components within Hashed al-Shaabi, which battled IS in Iraq, have for years been sending fighters to support the Syrian regime in its conflict with various rebel groups.

Even as leaders in both Iraq and Syria savour the setbacks inflicted by their forces on IS, they still need to examine the reasons that led to the formidable rise of the jihadist group.

After declaring "victory over brutality and terrorism" in Mosul, Iraqi Prime Minister Haider al-Abadi said there were "lessons to be learned" to ensure his country never again falls into the grip of IS.

"Huge mistakes have been made," he said.

- 'Reorganisation, redeployment' -

Syrian President Bashar al-Assad also faces huge challenges in the country's multi-sided war, despite his forces being backed by allies Russia, Iran and the Lebanese Shiite movement Hezbollah in the battle against jihadists and rebels.

IS fighters are steadily losing chunks of Raqa to the Syrian Democratic Forces (SDF), a US-backed Arab-Kurdish alliance which broke into the northern city in June.

A Russian-backed government offensive has also targeted IS forces in the central Syrian desert.

Analysts said that if Raqa falls, the Kurdish fighters that dominate the SDF could clash with regime troops.

Assad "does not want an autonomous administration" taking control of Raqa, said Syria expert and geographer Fabrice Balanche.

Ould Mohamedou said the war in Syria "goes beyond the question of IS," having erupted six years ago with peaceful anti-government protests that were brutally put down by the regime.

"In the name of the fight against Islamist terrorism, more and more Western governments have closed their eyes to the massacres perpetrated by the Syrian regime," he said.

The war in Syria has killed hundreds of thousands of people while millions more have been displaced in the two countries.

Rebuilding infrastructure and restoring stability to allow the displaced to return home will be a massive challenge.

The United Nations has said the level of destruction in Mosul alone is one of the largest and most complex challenges it has faced.

Unless all these challenges are tackled, IS jihadists driven out of territory in Syria and Iraq could re-emerge as a more brutal and formidable force.

For IS "the key words now are reorganisation and redeployment", said Guidere.

Ould Mohamedou said that even if IS is defeated in Syria and Iraq "it will bounce back elsewhere and... with a new look".

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