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David Petraeus speaks onstage during a fireside chat at the Team Rubicon Salute To Service Awards at Skirball Cultural Center on November 7, 2014 in Los Angeles, California. Imeh Akpanudosen, Getty Images

The greatest threat to long-term stability in Iraq is not Sunni militants with the Islamic State of Iraq and Syria (ISIS), but rather the Iranian-backed Shiite militias who have helped oust ISIS from parts of the country, General David Petraeus warned in an interview published Friday by the Washington Post.

Petraeus, who commanded U.S. troops during the height of America's war in Iraq, said the current situation there is "hard but not hopeless." He warned, though, that the Iranians will not play a constructive role in Iraq's future, despite the fact that the U.S. and Iran share a common foe in ISIS.

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"I would argue that the foremost threat to Iraq's long-term stability and the broader regional equilibrium is not the Islamic State; rather, it is Shiite militias, many backed by -- and some guided by -- Iran," he said.

"They prevented the Islamic State from continuing its offensive into Baghdad," he acknowledged. "Nonetheless, they have, in some cases, cleared not only Sunni extremists but also Sunni civilians and committed atrocities against them. Thus, they have, to a degree, been both part of Iraq's salvation but also the most serious threat to the all-important effort of once again getting the Sunni Arab population in Iraq to feel that it has a stake in the success of Iraq rather than a stake in its failure."

Left unchecked, the Shia militias could "emerge as the preeminent power" in Iraq, he said, "outside the control of the government and instead answerable to Tehran."

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Petraeus: Biggest threat to Iraq's future is Iran, not ISIS