(CNN) The biggest threat to Iraq's long-term stability isn't ISIS, according to Gen. David Petraeus, who led the U.S. surge during the Iraq War.

Instead, Petraeus said the Iran-backed Shiite militias who are helping to fend off ISIS are "the foremost threat" to long-term stability in Iraq, according to an interview with the Washington Post. The comments provide the most expansive glimpse yet into how Petraeus may be helping to shape the Obama administration's strategy in Iraq as he continues to advise the National Security Council on the issue.

Those militias, many funded and trained by Iran, have been an important part of efforts to push ISIS out of Syria, but they have also been accused of war crimes -- allegedly murdering not just ISIS fighters, but also Sunni civilians.

"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," Petraeus told the Post. "Longer term, Iranian-backed Shia militia could emerge as the preeminent power in the country, one that is outside the control of the government and instead answerable to Tehran."

Petraeus' comments come as the U.S.'s strategy to defeat ISIS is facing increased scrutiny on Capitol Hill as lawmakers debate how to enshrine the U.S.'s war against ISIS into legislation formally authorizing military force.

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