In the desert, Iraqis long viewed as an empty expanse exposed to sandstorms, smuggling routes, and military pursuits, a far more complex and unsettling narrative has now emerged: secret Israeli bases in Iraq. A shepherd was killed after allegedly seeing what he was never supposed to see, Iraqi forces reportedly came under fire, and official statements oscillated between denial and partial acknowledgment, as new layers of regional conflict unfold across Iraqi territory.
The lengthy investigation published by The New York Times into these bases was not merely a security account of a “secret site” deep in Iraq’s western desert. It appeared instead as a redrawing of the map of undeclared military influence inside Iraq, especially coming only days after a report by The Wall Street Journal that spoke of an Israeli base in the al-Nukhaib area. Between the two reports, a far more dangerous narrative began to emerge: Israel had not carried out a fleeting operation, but had instead established a temporary or semi-permanent operational infrastructure inside Iraqi territory in preparation for a regional confrontation with Iran.
The story, as recounted by The New York Times, began with a young shepherd named Awad al-Shammari, 29, who was moving through the open desert between his camp and the district of al-Nukhaib. There, entirely by chance, he came across an unusual military site: helicopters, soldiers, tents, and an airstrip. Such a scene, in an area supposedly under Iraqi surveillance, was enough to transform the shepherd from a passing witness into a target that had to be silenced, according to relatives and witnesses from the area.
According to the account published by the American newspaper, a helicopter pursued al-Shammari’s small vehicle and repeatedly opened fire on it until it came to a halt in the middle of the desert, where he was later found dead inside his burned-out car. More alarming still was the report’s claim that al-Shammari had informed Iraqi forces about what he had seen before contact with him was lost, meaning that the Iraqi military establishment had become involved in the heart of this story early on, rather than only after it surfaced in the media.
The report cites Iraqi and regional officials as saying that Israel used the base to support its operations against Iran, particularly during the “Twelve-Day War” in June 2025, by shortening flight distances and securing refueling, logistical support, and medical treatment for Israeli forces. In that sense, the issue is not merely about a limited intelligence presence, but rather an advanced operational platform inside Iraq, giving the matter an extremely sensitive sovereignty dimension.
More strikingly, the newspaper reported the existence of a second base whose location has yet to be disclosed, adding that preparations to establish secret sites in Iraq’s desert regions had begun in late 2024 in anticipation of any future confrontation with Iran. This particular point shifts the issue from the framework of a mere “security breach” to the possibility of a long-term Israeli strategy aimed at exploiting Iraqi geography as a rear arena in its conflict with Tehran.
Inside Iraq, however, official narratives were far from consistent, at times appearing contradictory to the point of confusion.
While The New York Times reported that an Iraqi reconnaissance force was dispatched to the site following the shepherd’s report, and came under fire that killed one soldier, wounded two others, and disabled two vehicles, the official Iraqi narrative sought to downplay the scale of the incident or redefine its nature.
The Joint Operations Command did acknowledge that Iraqi forces had been attacked by “foreign forces,” while the American report stated that the Iraqi army chief of staff contacted the US side and was informed that the force involved was “not American,” reinforcing Iraqi suspicions that it was Israeli.
Around ten days earlier, the Iraqi parliament had already moved in response to these reports, as an Iraqi official in Baghdad revealed that the ministers of defense and interior had been summoned to discuss international media reports concerning the existence of a secret Israeli military base in the al-Nukhaib desert, between Najaf and Anbar near the Saudi border.
While most lawmakers remained silent, MP Hassan Fadham made a striking statement to The Times, saying that “Israel has established at least one other military site inside Iraq,” adding that “the site in al-Nukhaib is the only one that has been discovered.” A second Iraqi official also confirmed the existence of another base in a western desert area, without specifying its location.
These statements suggest that part of Iraq’s political class has begun treating the Israeli presence as a reality on the ground rather than mere “media rumors.” At the same time, they open an extremely dangerous debate over the question of sovereignty: how was Israel able to establish operational sites inside Iraq without them being detected for such a long period? And was Washington aware of this?
According to The New York Times, senior Iraqi officials confirmed that military protocols require the United States to inform Baghdad of any military activity inside Iraqi territory. This means that Washington either deliberately concealed the Israeli activity, or that some Iraqi leaders believed the sites were American. In both cases, the Iraqi establishment appeared either outside the loop or relegated to its margins.
MP Waad al-Qaddo described what happened as “a blatant violation of Iraq’s sovereignty and the dignity of its people,” a phrase that encapsulates the scale of the political embarrassment generated by the affair, particularly in a country still navigating complex balances between American and Iranian influence.
From this perspective, the domestic dimension of the issue becomes more significant than its military aspect. The existence of Israeli bases, or even temporary operational units, inside Iraq provides Iran-aligned armed factions with enormous political and propaganda leverage. These factions can use the issue to justify maintaining their weapons and rejecting any governmental or American efforts to disarm them, under the banner of “confronting Israeli infiltration.”
This is what The New York Times itself hinted at when it reported that Iraqi anger over the presence of Israeli bases could threaten American efforts aimed at limiting Iranian influence inside Iraq.
Yasser Iskandar Watout, a member of the parliamentary Security and Defense Committee, said that what occurred was not the establishment of a new base, but rather the landing of an Israeli force at an old airstrip dating back to the era of Saddam Hussein’s regime. According to his account, the Israeli force had been searching for drone launch sites operating from Iraq. When Iraqi forces arrived at the location, they reportedly found no Israelis, but did discover leftover food and other traces behind.
This characterization attempts to shift the issue away from the idea of a “permanent base” toward that of a “temporary operation,” yet it implicitly acknowledges that an Israeli force did in fact enter deep into Iraqi territory and move within it before withdrawing.
The Iraqi government, meanwhile, appeared more inclined to politically contain the matter. Hussein Allawi, an adviser to outgoing Prime Minister Mohammed Shia’ Al Sudani, said that what occurred was merely an “airborne operation” aimed at retrieving something that had fallen from the sky during the war involving the United States and Israel on one side and Iran on the other. He added that intelligence provided by “a shepherd” had disrupted the mission after Iraqi forces moved toward the site.
Allawi also criticized what had been published by The Wall Street Journal, arguing that the newspaper was “trying to stir up issues,” and said that the Iraqi state had handled the incident through military and diplomatic channels with Washington and the international coalition.
What stood out in Allawi’s remarks, however, was that despite denying the existence of a “base,” he acknowledged that a real security incident had taken place and that a foreign force had operated inside the Iraqi desert. This suggests that the dispute is not over whether the incident occurred, but rather over how it should be described and the scale attributed to it.
Allawi also argued that reviving the issue in the media was intended to “create a rift between the Iraqi armed forces and the Iraqi people,” pointing to the public sensitivity surrounding any foreign breach of the country’s sovereignty.
In the same context, Karbala Operations Commander Ali Ghazi al-Hashemi denied the existence of any Israeli bases or camps in the deserts of Najaf and Karbala. Yet at the same time, he stated that “the force that was present in the Najaf desert in March was an Israeli force and did not remain for more than 48 hours.”
Here, the clearest contradiction in the Iraqi narrative emerges: nearly everyone denies the existence of “bases,” yet several officials acknowledge the presence of Israeli forces or Israeli operations on Iraqi soil. In other words, the real dispute is no longer over whether the incident happened, but rather over the nature of what happened.
But the core of the issue goes beyond the possibility of a hidden base or the movement of a foreign force across the desert. It also exposes the fragility of the security structure Iraq has spent years trying to rebuild after the war against ISIS. The state that repeatedly declared it had regained control over all its territory now finds itself facing a far more complex reality: vast borders, open deserts, and skies over which Baghdad does not exercise full
control, at a moment when Iraqi geography is once again becoming a stage upon which regional and international powers intersect and compete.
The Iraqi desert once again appears to have returned to its traditional role as an undeclared arena of conflict, where the military and intelligence calculations of regional powers overlap, and where different actors maneuver through security vacuums shaped more by the nature of the terrain than by the maps of sovereignty. Iraq thus emerges in an extremely sensitive position, caught between intertwined regional influence and intersecting international pressures, within an environment that does not grant it full control over all its trajectories.
Amid this entanglement, Baghdad finds itself facing a narrow political and security equation: either acknowledge the scale of the breach and the heavy sovereignty implications that come with it, or treat it as a limited incident, with all the accompanying risks of raising doubts about the state’s ability to control both its territory and its airspace. In either case, the greater challenge remains tied to the extent to which the Iraqi state can transform its sovereignty from a political declaration into a practical reality capable of being enforced.
Ultimately, the danger of what occurred lies not only in the accuracy of the circulating accounts or the contradictions between official and international narratives, but in whether Iraq truly possesses the ability to impose a coherent sovereignty framework capable of preventing its territory from becoming an operational arena or transit zone for the conflicts of others. What has emerged so far may be only the visible part of a broader and far more complex picture that has yet to fully unfold.
