There have been at least three explosions at Iraqi Shiite militia bases in the past month. The state-sanctioned militias, most of which receive backing from Iran, have fought alongside Iraq's regular armed forces against the Islamic State group.
Faleh al-Fayyadh said the statement by his deputy, Abu Mahdi al-Muhandis, did not represent the view of the mainly Shiite militias known as Popular Mobilization Forces - or the view of the Iraqi government.
Satellite photos of a destroyed site at a military base north of Baghdad, Iraq appear to confirm that the destruction was the result of an air strike.
In statements issued by his office, he also said that if Israel continues to target Iraq, the country "will transform into a battle arena that drags in multiple countries, including Iran".
Netanyahu did not directly name Iraq as one of those areas. A USA -led coalition provided crucial air support as Iraqi forces regrouped and drove IS out in a costly three-year campaign.
The United States maintains 5,000 troops in Iraq, and some groups such as the Hezbollah Brigades want them to leave.
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Israeli officials have also suggested recently that Iraq, whose main ally is Iran, has become more of a threat in recent years.
In a marked escalation in rhetoric, the Brigades issued a fiery statement later Thursday warning the USA that any new attack on an Iraqi position will be met with a harsh response.
"Be sure that if the confrontation between us starts, it will only end with your removal from the region once and for all", it said.
Two American officials said Israel carried out an attack on an Iranian weapons depot in July that killed two Iranian military commanders. The U.S. officials spoke on condition of anonymity because they were not authorized to discuss the matter with the media.
The base reportedly housed advisers for the Iranian-backed Lebanese Hezbollah group.
His deputy said the U.S. had brought four Israeli drones into Iraq to target the Popular Mobilisation's positions.
Iranian media reported a funeral for a "shrine defender" named Abolfazl Sarabian the next day, which typically denotes someone fighting in Iraq and Syria.
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An even bigger explosion at an arms depot at the al-Saqr military base near Baghdad on 12 August killed one civilian and wounded 29 others. The base housed a weapons depot for the Iraqi federal police and the PMF.
Israel has struck Iranian bases in neighboring Syria on numerous occasions, and there has been speculation that it might be expanding its campaign to target Iranian bases to Iraq.
A series of blasts in the past few weeks have hit weapon depots and bases belonging to paramilitary groups in Iraq, many of them backed by Israel's regional foe Iran. Netanyahu told a Russian-language outlet Thursday that the speculation is correct.
Asked about the destruction last week of an Iran-linked missile depot in southern Baghdad, Prime Minister Benjamin Netanyahu said, "Iran has no immunity, anywhere".
With the help of Iranian military advisers, weapons and funding, they prevented IS militants reaching Baghdad in 2014 and later helped Iraqi security forces regain control of the country.
The head of Iraq's paramilitary forces supported by Iran on Thursday walked back a statement by his deputy the day before in which he blamed Israeli drones and held the us responsible for a series of attacks on bases run by the militias.
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