(CNN) -- Bashar al-Assad's regime has lost control of much of Syria's long desert border with Iraq, as Sunni jihadist groups in both countries grow in strength, according to Western counter-terrorism officials and analysts.
The resurgence of al Qaeda in Iraq and the growing power of groups like the Nusra Front in Syria pose a broader threat: a cross-border alliance of militant Sunni groups capable of challenging governments in both Damascus and Baghdad and carving out a haven in a region where governments are struggling to exert control.
Last week, militants attacked a convoy of Syrian troops inside Iraq. According to some reports, the troops had entered Iraq for medical treatment. But the al Qaeda-affiliated Islamic State in Iraq, or ISI, claimed the Syrian soldiers had fled operations by "the brothers" in Syria. They were then ambushed near Akashat in Iraq's Anbar province as they were being escorted by Iraqi forces to the only border post the Syrian regime still controlled.
At least 40 Syrians and several Iraqis guarding them were killed in the ambush, which the ISI reported in distinctly sectarian terms, speaking of the "blood of the filthy ones from the Rafidah (Shiites)," in a statement issued to jihadist websites.
According to the ISI statement, the Syrian troops fled into northern Iraq after being forced to abandon a border crossing at al-Yarabiyah, a town at the northern end of the border that in more settled times saw scores of trucks pass to and from Iraq every day.
The Nusra Front began attacking a military base in al-Yarabiyah with mortars in late February, claiming that those who weren't killed "withdrew to the inside of the Iraqi borders," according to a translation by the SITE Intelligence Group.
The Free Syrian Army, which sometimes collaborates with the Nusra Front, said its forces were also involved in the attack, and several had been killed when Iraqi forces came to the aid of the besieged Syrian garrison.
According to Joseph Holliday at the Institute for the Study of War, recent events suggest not only growing coordination between al Qaeda and the Nusra Front, but a perilous situation along the border for the Assad regime.
"With three of four border crossing points impassible due to rebel gains in Syria, the Al Walid-At Tanf border crossing will be critical for the Assad regime and the Iraqi government to secure if they hope to maintain a ground line of supply between Baghdad and Damascus," Holliday says.
The Assad regime withdrew forces from a largely Kurdish area in northeast Syria last summer, weakening its control of the frontier in that area. In September, rebels seized the main crossing on the Euphrates River. Should the last crossing along the more than 600-kilometer (375-mile) border become insecure, Iranian efforts to reinforce the Assad regime would be hampered. Iran is al-Assad's main regional backer, while Iraq has expressed neutrality on the Syrian civil war.
Holliday says he believes the Iraqi and Syrian governments will be able to retain control of this last overland route, but if not, " the Assad regime will have to rely on air and sea resupply routes in order to continue its campaign against the opposition in Syria."
The Wall Street Journal reported Tuesday that in response to the deteriorating situation along the border, the Obama administration had authorized the CIA to step up cooperation with Iraq.
The newspaper reported: "In a series of secret decisions from 2011 to late 2012, the White House directed the CIA to provide support to Iraq's Counterterrorism Service, or CTS, a force that reports directly to Iraqi Prime Minister Nouri al-Maliki, officials said."
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Last week, a senior Iraqi official visiting Washington estimated that about 300 militants are crossing from Iraq into Syria every month, accusing the Gulf emirate of Qatar of helping finance the Nusra Front.
And on Tuesday, U.S. Director of National Intelligence James Clapper warned that the Nusra Front has "gained strength" in Syria. He said the group had been "astute," providing humanitarian services to win over the population while bringing in foreign fighters.
Sunnis in northern Iraq have staged a number of protests in recent weeks against the central government, which is dominated by a coalition of Shia parties led by al-Maliki. Faleh al Fayad, Iraq's national security adviser, told al Monitor newspaper last week that "events in Syria have taken on a sectarian dimension, which will certainly influence Iraq due to the country's diverse sectarian composition."
At the same time, Fayad acknowledged that the "Iraqi security apparatus still suffers from the technical void left behind by the Americans."
The U.S. State Department has already asserted close links between the Nusra Front and al Qaeda in Iraq, as the ISI is also sometimes known. In December, it designated al Nusra as an alias for the group, saying al Nusra "has sought to portray itself as part of the legitimate Syrian opposition while it is, in fact, an attempt by AQI to hijack the struggles of the Syrian people for its own malign purposes. AQI emir Abu Du'a is in control of both AQI and al-Nusra."
Nada Bakos, a former CIA agent, told CNN in January that Syrians were among the inner circle of al Qaeda in Iraq when it was led by the Jordanian Abu Musab al Zarqawi.
Bakos, who was the chief targeting officer tracking Zarqawi, said: "Some of these commanders are probably now part of al-Nusra," and the two groups are likely to replicating the flexible and resilient networks he established. That makes them a force to be reckoned with, she believes.
An analysis published by the Quilliam Foundation in January also found that the Nusra Front is led by veterans of the Iraqi insurgency. Indeed, the Assad regime's tolerance of militant groups using Syrian soil as a conduit to supply the militant groups in Iraq may well be returning to haunt it.
Zarqawi built up an infrastructure in Syria, establishing safe houses in Syria from which thousands of volunteers -- including many Syrians -- traveled to fight in Iraq. The group's Syrian commanders were also the key channel for financial contributions from the Saudi and Gulf region, according to the Quilliam Foundation.
Under Abu Du'a's leadership, the ISI has stepped up sectarian attacks against Shiite targets in Baghdad and elsewhere with a series of suicide bombings and assassinations.
Analysts believe the Nusra Front's hostility to the West could create an "over-the-horizon" threat to the United States and its allies if the group is able to secure a foothold in Syria and across the Levant.
In such a scenario, al Qaeda-aligned groups would operate close to Arab borders with Israel, improving their potential to launch a direct attack against the country, long an objective of Ayman al-Zawahiri, al Qaeda's current leader.