Blast latest in series of explosions targeting sites belonging to groups under umbrella of Popular Mobilisation Forces.
The attack marks a significant escalation in Israel’s years-long campaign against what it sees as Iranian military assets in the region.
The confirmation comes as Israeli Prime Minister Benjamin Netanyahu strongly hinted that his country was behind recent air raids that have hit bases and munition depots belonging to Iran-backed paramilitary forces operating in Iraq.
The mystery attacks have not been claimed by any side and have left Iraqi officials scrambling for a response amid strong speculation that Israel may have been behind them.
Earlier this week, the deputy head of the Iraqi Shia militias, known collectively as the Popular Mobilization Forces, openly accused Israeli drones of carrying out the attacks, but ultimately blamed Washington and threatened strong retaliation for any future attack.
Such attacks are potentially destabilising for Iraq and its fragile government, which has struggled to remain neutral amid growing tensions between the United States and Iran.
Al Jazeera’s Natasha Ghoneim, reporting from Baghdad during the latest round of air raids, said Iranian-backed armed groups have been operating in Iraq with the full support of the government since 2014 when they joined the fight against the Islamic State of Iraq and the Levant (ISIL or ISIS) group.
“A new law that came into effect on July 31 requires all paramilitary groups to report to the Iraqi security forces, or put down their weapons,” Ghoneim reported.
There have been at least three explosions at Iraqi Shia militia bases in the past month. US officials now confirm Israel was responsible for at least one of them.
Two US officials said Israel carried out an air raid on an Iranian weapons depot in July that killed two Iranian military commanders. The US officials spoke on condition of anonymity because they were not authorised to discuss the matter with the media.
The July 19 attack struck a militia base in Amirli, in Iraq’s northern Salaheddin province, causing a huge explosion and fire.
A senior official with the Shia militias at the time told AP that the base hit housed advisers from Iran and Lebanon.
He said the attack targeted the headquarters of the advisers and a weapons depot.
On August 12, a large explosion at the al-Saqr military base near Baghdad shook the capital, killing one civilian and wounding 28 others.
The base housed a weapons depot for the Iraqi federal police and the PMF. The most recent of the explosions came on Tuesday night, at a munitions depot north of Baghdad.
There have been weeks of speculation in Israel that the army is attacking targets in Iraq.
In an interview with a Russian-language TV station on Thursday, Netanyahu indicated the speculation is true.
“I don’t give Iran immunity anywhere,” he said, accusing the Iranians of trying to establish bases “against us everywhere”, including Syria, Lebanon, Yemen and Iraq.
Asked whether that means Israel is operating in Iraq, Netanyahu said: “We act in many arenas against a country that desires to annihilate us. Of course I gave the security forces a free hand and the instruction to do what is needed to thwart these plans of Iran.”
Early on Friday, the New York Times, citing Israeli and US officials, reported that Israel bombed an Iranian weapons depot in Iraq last month.
It would be the first known Israeli air raid in Iraq since 1981 when Israeli warplanes destroyed a nuclear reactor being built by Saddam Hussein.
It also steps up Israel’s campaign against Iranian military involvement across the region.
Israel has previously acknowledged hundreds of air raids on Iranian targets in neighbouring Syria, primarily arms shipments believed to be destined for Iran’s Hezbollah allies.
Israel considers Iran to be its greatest enemy and has repeatedly promised that it will not allow the Iranians, who are supporting the forces of Syrian President Bashar al-Assad, to establish a permanent military presence in Syria.
Striking Iraq would be far more complicated than reaching neighbouring Syria.
Israel and the Saudis do not have formal diplomatic relations but are believed to have established a behind-the-scenes alliance based on their shared hostility towards Iran.