Israel is known to have struck Iranian targets in Syria on numerous occasions - as well as in Lebanon and Sudan in the past.
"We're acting not only if required, we're acting in very many theatres against a state that seeks to annihilate us. Of course I gave the security forces a free hand and instructed them to do anything necessary to thwart Iran's plans", Netanyahu responded, as reported by Reuters news agency.
He added that he led, and, in many aspects was "still leading the world's efforts to neutralize the Iranian threat". "And there were years when I stood alone".
There was no immediate comment from government officials to the PMF statement, which appears to have been issued without prior consultation with Iraqi security forces - an embarrassing sign of how the militias operate independently.
His deputy said the United States had brought four Israeli drones into Iraq to target the Popular Mobilisation's positions.
Two Iranians were reportedly killed by a blast at a base in Amerli, also in Saluhddin, on 19 July. "We will act - and now are acting - against them, wherever it is necessary", he declared.
US officials have confirmed that Israel was responsible for the bombing of an Iranian weapons depot in Iraq last month, an attack that would mark a significant escalation in Israel's years-long campaign against Iranian military entrenchment across the region.
Associated Press meanwhile reported that an Iraqi government fact-finding committee had concluded the explosion was the result of a drone strike. The US initially said they would comply, but have since disavowed this. The attack was followed by at least two other mysterious explosions at munitions depot near Baghdad belonging to the militias.
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"The Hashed al-Shaabi targeted a surveillance drone flying over the Brigade 12 base in the Baghdad belt, forcing it to withdraw without finishing its surveillance mission", the group said in an online statement.
Al-Saqr was among a string of explosions that hit militia bases and munitions depots over the past several weeks.
The attacks represent a new front for Israel, having previously focused on targeting Iranian positions in Syria.
If Israel did carry out the bombings, it would be an expansion of its campaign against Iran's spreading influence in the region.
Striking Iraq would be far more complicated than reaching neighboring Syria.
A senior Middle Eastern intelligence official said that Israel had bombed a base north of Baghdad on July 19. They spoke on condition of anonymity because they were not authorized to speak about the issue.
USA officials have confirmed Israel was responsible for the bombing of an Iranian weapons depot in Iraq last month.
Former Iraqi Prime Minister Nouri al-Maliki is warning of a "strong response" if it is proven that Israel was behind recent airstrikes in Iraq.
A Western diplomatic source reportedly told a Saudi-owned newspaper Wednesday that Israel has conducted several strikes on Iranian-controlled bases in Syria and Iraq with permission from the United States and Russian Federation. He said the attack targeted the headquarters of the advisers and a weapons depot, causing a huge explosion and fire.