Billboard bearing the portraits of slain Iranian revolutionary guards generals Hossein Salami (L), Mohammad Bagheri (C) and Gholamreza Mehrabi, who were killed by recent Israeli strikes.

Middle East Eye – Aug 4, 2025

When Israel launched a surprise 12-day assault on Iran in June, Tehran and the world were caught off guard. Few anticipated such a move, particularly while Iran was engaged in sensitive nuclear negotiations with the United States.

Sources told Middle East Eye that a handful of countries had warned Iranian authorities about suspicious Israeli movements. Yet despite heightened alert levels, Tehran was ultimately blindsided when the attack materialised.

The nature of the attack and the ease with which it was executed sent shockwaves through Iran’s political and security establishment. Behind the scenes, covert Mossad agents, paid informants, and a network of operatives – many allegedly embedded among Afghan migrants – are believed to have facilitated the strikes.

An Iranian source in the conservatives’ camp told MEE that Israel had long stationed agents inside Iran, observing the movements of officials. The source added that a series of cyber intrusions into Iranian banks and government institutions may have compromised personal data – including phone numbers and addresses of high-level figures and their families – paving the way for deeper penetration.

“There have been some Eli Cohens inside the Islamic Republic too,” the source remarked, referencing the infamous Israeli spy executed in Syria.

The Cohens 

In 2021, former president Mahmoud Ahmadinejad publicly revealed that the head of the Israeli desk at Iran’s Ministry of Intelligence had, in fact, been a Mossad agent – and was later arrested.

“How could the top official responsible for tracking Israeli spies turn out to be one himself?” Ahmadinejad asked at the time. “Is it even conceivable that a single person was solely running Israeli operations inside Iran, without any oversight or team?”

Just four days into the war, on 17 June, Israel killed Iran’s highest-ranking military officer, Ali Shadmani, who was leading the Khatam al-Anbiya headquarters – effectively the country’s war command centre.

Shadmani’s daughter told Iranian media: “My father was martyred in a direct confrontation with the Zionist regime.”

“Many assume he died in a random air strike, but he was assassinated in a targeted operation.”

She added that after his death, Hebrew-language media celebrated the killing of the Islamic Republic’s “war commander” and “closest military figure to the Supreme Leader.”

Further revelations came from Fayaz Zahed, a member of the Government Media Council, during a televised interview.

Zahed cited three separate incidents to highlight what he described as deep Israeli infiltration into Iran’s security establishment.

In the first, he said IRGC commander Hossein Salami warned the head of Iran’s state broadcaster, Peyman Jebelli, at 1:30 am on 13 June, the first day of the war, that Israel was planning an attack that night. Salami was killed in an Israeli strike just 90 minutes later,  suggesting that senior Iranian officials may have been aware of the impending attack but were unable – or failed – to prevent it.

In another case, Zahed questioned who had directed IRGC intelligence chief Mohammad Kazemi to the building that was struck by Israel two days later, implying that Mossad agents had deliberately led him into the trap.

Zahed also referred to a third incident, in which nine Revolutionary Guard generals were reportedly gathered at the Joint Chiefs of Staff. He said Israel appeared to have known about the meeting in advance and waited until a tenth general arrived before launching the strike.

“The claim that nine people were gathered in a meeting at the Joint Chiefs of Staff, and that the operation began only after one person’s delayed arrival, is no trivial matter,” he said.

“The Ministry of Intelligence and IRGC intelligence must conduct a serious and thorough investigation. Without addressing the root of the problem, there’s no guarantee it won’t happen again. The culprits may still be in place, ready to finish what they started.”

A key vulnerability, according to insiders, has been the influx of undocumented Afghan migrants into Iran.

“Afghans in Iran are not Israeli spies,” one source in government said, “but the large number of undocumented individuals who crossed illegally, particularly after the Taliban took power, created a major opportunity for Israeli intelligence.”

Former president Ebrahim Raisi’s decision to open Iran’s borders at the time is now being viewed in retrospect as a major security miscalculation.

The source added that some Afghan migrants were unknowingly paid by Israeli operatives to assemble parts later used in drone attacks from within Iranian territory.

“They didn’t know who they were working for – they were just following instructions,” he said.

Infiltration from within

One former security official described to MEE how Israel began penetrating Iran’s intelligence infrastructure nearly two decades ago by exploiting “ideological vulnerabilities” within the system.

He pointed to the election of Ahmadinejad in 2005 as a turning point.

“That period saw a rupture in the intelligence apparatus. Many of the seasoned experts who had gained experience during the 1980s were pushed aside. A new generation – lacking field experience – took over. That significantly weakened us,” he said.

He added that the early 2000s also saw the expansion of Israeli intelligence bases in neighbouring countries.

Following the 2009 Green Movement protests – labelled “sedition” by hardliners – many individuals advanced rapidly through the security ranks by demonstrating loyalty to the supreme leader and hostility toward the protests.

“That environment likely allowed foreign assets to rise through the system unnoticed,” the source said.

He also criticised the ideological shift in Iran’s security focus: “The more ideological the system became, the more it prioritised cracking down on unveiled women and dissidents instead of foreign spies.”

The source noted that, “The emergence of overlapping and competing security bodies further fragmented the intelligence landscape, leading to internal confusion and jurisdictional conflicts.”

Fallout and suspicion

In the weeks following the war, the Ministry of Intelligence issued a statement declaring that it had thwarted assassination plots against 23 senior officials and arrested 20 Mossad agents.

Meanwhile, one name has surfaced in the public’s mind: Ali Shamkhani, the former head of Iran’s Supreme National Security Council and an adviser to the supreme leader, who was initially thought to have been killed in an Israeli strike. He later appeared on state television unharmed, claiming he had been trapped under rubble for hours – a statement that fuelled rumours and suspicion.

“I looked closely at his face on TV,” said former MP Gholamali Jafarzadeh Imenabadi. “There was no sign that he’d been trapped under rubble for three hours.”

MP Ahmad Bakhshayesh Ardestani further fuelled speculation, saying: “There are serious ambiguities about Mr. Shamkhani’s case. Some claim his son warned him to leave the building before the attack even began.”

Notably, two of Shamkhani’s aides have been arrested in the past decade on charges of spying for Israel.

As the dust settles from Israel’s most controversial operation in years, Iran’s intelligence and political leaders face growing pressure to account for what many now believe was a deep and long-running infiltration – one that may not yet be over.

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