BAGHDAD — It was a tense confrontation between two forces supposed to be on the same side in Iraq.
First, heavily armed police, led by the interior minister, waded into a Shi’ite militia base south of Baghdad and arrested its deputy commander, accused of organizing attacks on Sunni mosques. They loaded the man, Ali Reda, into an armored sport utility vehicle.
Then militia reinforcements descended, surrounded the police, and demanded Reda be freed. Weapons were drawn. The minister, Mohammed al-Ghabban, the highest figure in Iraq’s police force, frantically called Baghdad from inside his SUV.
In the end, Ghabban surrendered his prisoner and left empty-handed, angry and humiliated.
The standoff in mid-January, described by six officials and militia leaders, was a stark example of the power that Shi’ite militias have accrued in Iraq and their boldness in wielding it.
These militias, many of them backed by Iran, mobilized in 2014 to fight Sunni extremists from the Islamic State. However, they are now showing no intention of standing down after the battle, demanding instead to be a major force shaping Iraq.
That prospect worries not only Iraq’s Sunni minority but also officials in the military and the Shi’ite-led government, who fear the militias will dominate Iraq the way the Revolutionary Guard does Iran and the guerrilla group Hezbollah does Lebanon.
Two top generals warned that the army could eventually come to blows with the militias, known collectively as the ‘‘Hashd,’’ Arabic for ‘‘mobilization.’’
‘‘They [the militias] have now infiltrated the government and are meddling in politics,’’ said Ali Omran, commander of the army’s Fifth Infantry Division and a veteran of numerous battles against the Islamic State. ‘‘I told the Hashd people that one day I and my men may fight them.’’
The more than 50 Shi’ite militias in Iraq have between 60,000 and 140,000 fighters, according to estimates from the government and the Hashd itself. They are backed by tanks and weapons, and have their own intelligence agency, operations rooms, and court of law.
The larger militias, like Asaib Ahl al-Haq, the Hezbollah Brigades, Badr, and the Peace Brigades, have been in place since soon after the 2003 ouster of Saddam Hussein. They are linked to political parties, effectively forming armed branches for politicians.
But the ranks of the militias swelled dramatically after ISIS overran nearly a third of Iraq in the summer of 2014 and Grand Ayatollah Ali al-Sistani, Iraq’s top Shi’ite cleric, called on able-bodied males to fight the Islamic State. At the time, tens of thousands turned out.
Those same militias now want to remain a permanent, independent armed force and are resisting attempts to integrate them into the military or police, according to interviews with more than 15 government officials, army generals, and militia leaders and visits to Tikrit and Samarra, Sunni-majority areas where the militias now hold power. The militias insist they have earned a special status, pointing to the 5,000 militiamen killed and 16,000 wounded fighting ISIS.
‘‘Those who sacrificed more are entitled to more,’’ said Hamed al-Jazaeery, head of the al-Khorasani Brigades militia. ‘‘What is written with blood cannot be removed.’
Jazaeery wears the black turban of a cleric and the camouflage fatigues of a fighter. The walls of his office are adorned with photos of the leader of Iran’s Islamic Revolution, Ayatollah Ruhollah Khomeini, and its current supreme leader Ayatollah Ali Khamenei. Other photos show Jazaeery posing with General Qassem Suleimani of Iran, the powerful Revolutionary Guard figure who helped organize the Iraqi militias against the Islamic State.
‘‘We want to be a third power in Iraq,’’ alongside the army and police, Jazaeery said. ‘‘Why can’t the Hashd be like the Revolutionary Guard in Iran?’’