Two weeks after launching an all-out offensive to retake Fallujah from Islamic State fighters who have held the city since 2014, Iraqi government officials declared victory over the weekend after government troops recaptured the center of the city. Though sporadic fighting continues in a few outlying districts, reports suggest most of the militants have fled. Now the question is what happens next.

That's important because Fallujah, where U.S. forces fought bloody battles in 2004 against al-Qaida, ISIS' predecessor, is a microcosm of Iraq's deep sectarian divides and the political crisis created by the Shiite-led Iraqi government's failure to address the demands of the country's Sunni minority for greater local autonomy and revenue sharing. Unless Iraqi Prime Minister Haider al-Abadi can reassure disaffected Sunnis that he is committed to an equitable power-sharing arrangement that benefits all of Iraq's citizens, the government's gains on the battlefield are unlikely to translate into a lasting peace.

Unlike his predecessor, former Prime Minister Nouri al-Maliki, Mr. al-Abadi seems to recognize that having taken Fallujah, his government must make every effort to avoid reprisals against local residents, rein in the Iranian-backed Shiite militias that helped U.S.-trained Iraqi special forces units capture the city, and protect the tens of thousands of civilians who were forced to flee their homes by the fighting. Human rights groups have accused the Shiite paramilitary units of widespread human rights violations related to the arrest, torture and murder of Sunnis fleeing Fallujah and its outskirts.

Mr. al-Abadi has taken some steps to hold the militias accountable for those abuses, but many of the units aren't fully under the government's control because they're recruited and funded by Iran. That undermines the Sunni minority's confidence that the government is willing or able to protect them and perpetuates the cycle of violence and reprisals that has weakened the central government's authority in the areas formerly controlled by ISIS.

Last week, the government announced it had launched an investigation into allegations of human rights abuses against civilians fleeing Fallujah by Shiite militias. A government spokesman said arrest warrants had been issued for some militia members and that the prime minister was closely monitoring the results, but he did not provide any details about whether those arrested were from the Iraqi army special operations forces or the militias. If Mr. al-Abadi hopes to regain the trust of Fallujah's residents, he must take decisive action against militias implicated in atrocities

He also needs to forge a genuine power-sharing arrangement with the Sunni minority that gives them an equitable stake in the country's future. Under the winner-take-all politics of former Iraqi dictator Saddam Hussein, the Sunni minority held virtually all the top jobs in the government, the military and the private sector — all privileges it lost after the U.S. invasion in 2003. Mr. al-Abadi admittedly faces a difficult balancing act in attempting to re-empower the Sunni minority after years of discrimination and political disenfranchisement. But it is the only way to unify his country against the continuing threat from ISIS.

With the fall of Fallujah, ISIS has been driven from its last major stronghold in Iraq except for the northern city of Mosul, which the government intends to retake next. That battle promises to be an even more difficult affair than the struggle to recapture Fallujah, requiring a coordinated effort of not only Iraqi special forces and Shiite militias but also Kurdish fighters who hope to make the city the capital of an autonomous Kurdish homeland. And they will want the same kinds of guarantees of local autonomy and control over revenues that the Sunni minority in Fallujah wants.

Negotiating those conflicting demands will severely test Mr. al-Abadi's leadership in the coming months, as well as the U.S. strategy for stabilizing the country through limited airstrikes and intelligence and logistics support for local units on the ground. But none of those measures can prevent Iraq from sliding further into chaos unless its leaders recognize the need for a process of political reconciliation that affords all Iraq's varied sectarian and ethnic factions a fair say in their country's future.