NAJAF, Iraq — From his modest office in the shrine city of Najaf, Iraq’s highest religious authority, Grand Ayatollah Ali al-Sistani, leader of the country’s Shiite establishment, issued a call to arms asking his followers to join with the government military to stop the blitzkrieg by the Islamic State in Iraq and Syria.

But one cleric, Moktada al-Sadr, who led a militia that fought the government and lost in 2008, decided instead that he too would challenge the state. Mr. Sadr revived his Mahdi Army, possibly one of the largest and most experienced battle groups in Iraq, and announced that under no circumstances would it be under the control of the government.

His open challenge to Iraq’s Shiite establishment lays bare the latest in a series of cracks that are dividing the country’s three main ethnic groups, the Shiites, Sunnis and Kurds, as the Iraqi state comes unraveled. But as Mr. Sadr’s actions show, the fault lines are not strictly between religious and ethnic groups, but also within each group, a fracturing that could lead Iraq to even greater chaos and uncertainty.

After the United States military invasion of Iraq in 2003, the Shiite south was badly divided among different factions, including those loyal to Ayatollah Sistani and Mr. Sadr. But in recent years, largely because of Ayatollah Sistani’s efforts, militias were disbanded and a rocky unifying process was underway. For a time, it appeared as if Shiites might behave as a unified force with a Shiite-controlled government in Baghdad and a revered religious figure, Ayatollah Sistani, coaxing them to work together.