12JUN

Israel ran covert bases in Iraq

3 min read

09:18UTC

The New York Times and Wall Street Journal reported that Israel operated two covert military bases in Iraq's western desert since late 2024; Iraq protested privately to Washington in March.

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ConflictDeveloping

Key takeaway

Israel has run covert Iraqi bases since 2024; Baghdad protested privately, six weeks before disclosure.

The New York Times (NYT) and Wall Street Journal (WSJ) reported on 18 May that Israel operated two covert military bases in Iraq's western desert from late 2024, with one base near Najaf and Karbala roughly 100 kilometres south-west of Baghdad and close to the Saudi border. The bases functioned as Israeli special-forces housing, an air-operations logistics hub, and search-and-rescue staging for downed pilots. The WSJ added that one base 'operated with the knowledge of the United States'; US officials denied direct involvement. Iraq publicly denied authorising any foreign military presence. The same Iraqi officials had privately protested to Washington in late March 2026, six weeks before the disclosure, according to the NYT. Baghdad absorbed the violation silently across that window, without an Iraqi parliamentary debate. Iraq runs a 329-seat Council of Representatives in which Iran-aligned factions hold a working bloc; a public protest would have triggered a no-confidence motion against Prime Minister Mohammed Shia al-Sudani, which the private channel was engineered to avoid. The covert-basing date pre-dates the 28 February strike by 14 months. The 'joint Israel-US surprise' framing that has organised public coverage of the war since Day 1 sits awkwardly against a prepared forward-basing infrastructure with western Iraq as its rear area. Hui Chuan's seizure outside Fujairah and the broader Hormuz interdiction tempo sit inside the same pre-staged operational picture, which means the planning horizon is now visibly longer than the operational tempo had suggested. Baghdad's late-March protest was absorbed by Washington without public disclosure, six weeks before the NYT and WSJ broke the story. The diplomatic management appears engineered to survive the kind of host-state protest that normally forces public renegotiation: a private demarche on a covert base built fourteen months in advance, against a NATO partner-of-convenience whose 329 parliamentarians have not yet been notified at the time of publication. Iraq also runs the bilateral Hormuz passage system Foreign Minister Abbas Araghchi codified in mid-May , making the sovereignty breach a live commercial as well as political problem for Baghdad.

Deep Analysis

In plain English

Israel secretly operated two military bases inside Iraq without Iraqi government authorisation. The bases, discovered in the western Iraqi desert, were used to house Israeli special forces and to support search-and-rescue missions for downed Israeli pilots during strikes on Iran. Iraq publicly denied knowing about them and privately complained to Washington. This matters because Iraq is technically not a party to the current conflict. Having Israeli forces operating from its soil, without permission, puts Baghdad in an impossible position: it cannot ignore it without looking complicit to Iran-aligned groups inside Iraq, and it cannot expel the forces without risking US displeasure.

Deep Analysis

Root Causes

Israel's preemption doctrine requires forward staging close to Iran's western flank, and the western Iraqi desert offers the only land-based proximity available without crossing Jordanian or Saudi territory.

Iraq's post-2003 sovereignty deficit, the gap between Baghdad's formal authority and Washington's actual control of basing decisions, has structurally allowed host-state protests to stay private rather than escalate to public renegotiation. The United States accepts a deniability buffer between Tel Aviv and Tehran that lets Israeli operations proceed without American forces being directly implicated.

Iran's IRGC-Quds Force presence in southern Iraq creates a targeting requirement on the Israeli side that 14 months of advance basing was designed to service. Each driver sits independently upstream of the bases; together they explain why Baghdad's March 2026 protest produced silence rather than withdrawal.

What could happen next?

Risk
Iran-aligned militias in Iraq will use the disclosure to justify retaliatory strikes against US forces at Al-Asad and Ain Al-Asad air bases, framing them as legitimate targets for aiding Israeli operations.
Immediate · 0.72
Consequence
Baghdad's private Washington protest may escalate to a formal parliamentary resolution demanding US troop withdrawal, destabilising the CENTCOM logistics network for Hormuz operations.
Medium term · 0.58
Precedent
The normalisation of covert Israeli military presence in Arab states without formal agreement sets a new baseline for shadow-alliance architecture in the post-Abraham Accords Middle East.
Long term · 0.65

Source Landscape

This story draws on mixed-leaning sources from Qatar

Qatar

Primary parallel: Jordan's covert hosting of US and Israeli intelligence liaison units in the late 1990s and early 2000s, a relationship exposed progressively through leaks rather than any formal disclosure, follows the same pattern: a state adjacent to Israel quietly accommodating Israeli operational presence in exchange for security guarantees, with deniability built into the arrangement. Jordan's experience shows this kind of relationship can persist for years before public rupture.

Counter-parallel: The 2020 Abraham Accords normalisation framework provides a counter-case: states that formally acknowledged Israeli operational relationships saw those relationships become politically durable. Iraq, lacking any normalisation framework and governed by Iran-aligned coalition parties, has no equivalent mechanism for managing disclosure, making the political blowback structurally more dangerous.

Consensus view: RAND Corporation's Dalia Dassa Kaye and Chatham House's Lina Khatib both assess the Iraqi base disclosure as the most significant sovereignty rupture in the region since the 2019 US withdrawal from northern Syria.

The bases near Najaf and Karbala sit in Shia-majority territory within 100 kilometres of Baghdad, a location Iran-aligned militias such as Kataib Hezbollah treat as their domestic sphere. Any Israeli special-forces presence there was necessarily tolerated at some level by Iraqi security structures or their backers.

Counter-view: Stratfor's Middle East desk and the International Institute for Strategic Studies (IISS) argue the bases' existence in Iraq's western desert does not necessarily imply Baghdad's knowledge: Iraq's Anbar and southern desert zones have historically hosted unacknowledged foreign operations (Jordan, Saudi Arabia, US SOF) without central government awareness.

Iraq's private March 2026 protest to Washington, rather than a public expulsion, signals it learned of the presence after the fact rather than authorising it.

Key tension: Whether Iraq's government had any prior knowledge determines whether this constitutes a bilateral intelligence failure between Baghdad and Washington or a deliberate deception of an ostensible ally.

First Reported In

Update #101 · Barakah hit, Trump posts, Italy sends minesweepers

Al Jazeera (citing NYT/WSJ)· 18 May 2026

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Causes and effects

Caused by

Floating armoury seized 38nm off Fujairah

The Hui Chuan seizure outside Fujairah is part of the same pre-staged operational picture that the Iraq base revelation now makes explicit.

Occurred 14 May 2026

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This Event

Israel ran covert bases in Iraq

Pre-staged forward basing 14 months before the 28 February strikes rewrites the war's planning horizon and quietly violates Iraqi sovereignty.

Different Perspectives

Oil markets and Lloyd's of London

Brent fell to $89.25 on ceasefire probability, not new barrels, with traders voting for Trump's deed over Tehran's denial. Lloyd's has not repriced Hormuz war-risk cover because its trigger requires a UN Security Council resolution or government certification, so tanker insurance costs remain elevated regardless of the spot move.

Pakistan and Qatar mediators

Pakistan's Mohsin Naqvi was in Tehran for his second visit in under a week, using the Pakistan-Qatar channel that delivered April's ceasefire after an identical public-denial cycle. The channel carries both civilian and military buy-in from Islamabad, the only configuration Iran's split command cannot dismiss as a partial signal.

India

India summoned the US Deputy Chief of Mission after three Indian sailors were killed aboard MT Settebello, the first formal grievance from a major non-belligerent directed at US enforcement. Indian seafarers supply roughly 12 per cent of the global maritime workforce; their presence on third-flag Gulf tankers is structurally inevitable regardless of bilateral diplomacy.

Islamic Revolutionary Guard Corps (IRGC)

The IRGC declared Hormuz closed on 11 June while civilian negotiators were on the same mediation channel, then issued no public comment on the MoU framework. Its silence on the framework, rather than any foreign ministry statement, is the operative approval signal; the corps' unilateral Hormuz closure shows it did not treat the diplomatic track as binding on its operations.

Iran foreign ministry (Baghaei)

Esmail Baghaei told IRNA that reports of a finalised deal were 'merely speculation' and that Iran had 'not yet made a final decision'. The denial is structurally identical to Iranian foreign ministry statements during the April ceasefire talks, which produced a binding text within 48 hours of the same language.

Trump administration / CENTCOM

Trump cancelled the third strike day and called the MoU 'very strong' and almost ready to sign, while CENTCOM kept tanker enforcement running in the same 24-hour window. The administration is simultaneously withdrawing the military pressure it claims drove the deal and sustaining the enforcement campaign it is trying to trade away.