US President Barack Obama has said he would authorize military forces to overthrow Syrian President Bashar Assad if regime troops attempt to shoot down American planes as they strike Islamic State targets in Syria, according to a New York Times report.

The move would represent a significant shift in Washington’s stated aims in Syria and Iraq, where a campaign of airstrikes has been planned to thwart the advance of the IS jihadi group. It also highlights the tangle of alliances and antagonisms in the war-torn region, where the US and Syria, while not allies, find themselves both fighting the same foe.

Citing members of a group of people who met with Obama in a closed meeting last week, The New York Times reported that the president said he would wipe out Assad’s air defense system if he tried to hit American planes. The move, he said, would lead to Assad’s overthrow, according to the newspaper’s account.

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Syria’s air defenses have taken a major hit in the country’s north and east, but the air force is still active, firing rockets and dropping crude bombs on rebel-held areas on daily basis.

Obama called on Wednesday for a “systematic campaign of airstrikes, hitting IS targets as Iraqi forces go on the offensive.” He said American bombers would not hesitate to hit IS in Syria, even though, unlike Iraq, it had not requested assistance.

He added that in the fight against the Islamic State group, the US “cannot rely on an Assad regime that terrorizes its own people — a regime that will never regain the legitimacy it has lost,” insisting rather that strengthening the opposition is “the best counterweight to extremists like ISIL, while pursuing the political solution necessary to solve Syria’s crisis once and for all.”

On Sunday, US Secretary of State John Kerry said the US would not coordinate airstrikes with Assad, but added that other countries in the region had offered to help militarily. The New York Times reported Sunday that Arab countries had proposed carrying out airstrikes against the Islamic State.

The fight against IS in Iraq has also put the US alongside Iran, in another show of the region’s shifting alliances, but on Monday, the US State Department said it was opposed to military cooperation with Iran in Iraq but was open to further talks, hours after Tehran said it had rejected US overtures to help in the fight against jihadists.

“We are not and will not coordinate militarily… There may be another opportunity on the margins in the future to discuss Iraq,” US State Department spokeswoman Jen Psaki told reporters shortly after the end of a major Paris conference on the issue, to which Iran was not invited.

Obama’s choice to fight IS in Syria after not backing more moderate groups in Syria trying to overthrow Assad for the past three years has raised questions as to whether US strikes will serve to empower Assad to continue his brutal assault on rebel groups.

“It gives him the license to actually become a lot more aggressive,” said Haras Rafiq of the Quilliam Foundation, a London-based think tank.

Rebel activist Abu Yazan, based in eastern Damascus province, said supporting the armed opposition was crucial for winning the hearts and minds of Syrians living in areas controlled by the Islamic State group.

“If you only fight the Islamic State, and the regime drops barrel (bombs) on those areas, it’s hard to convince people to support (the US airstrikes) because they will see it as supporting Assad,” he said.

There is also concern that short of toppling Assad and clearly backing the moderate Free Syrian Opposition, there is no way to ensure that should the US chase IS out of its strongholds, the vacuum won’t be filled by either Assad or other jihadist elements.

“There’s no debate that the Americans can hit from the air, but the big question is, will they do it without the opposition to take the areas after they have been hit?” said Hassoun Abu Faisal, an Aleppo-based activist.

Aron Lund, a Swedish researcher on Syrian groups, said it remained to be seen whether US airstrikes would end up helping the Assad government or the rebels.

“If the US manages to roll back the Islamic State from areas like in Aleppo or Hassakeh, then that vacuum needs to be filled by somebody,” Lund said. “The Islamic State captured those areas by default because they were the strongest group to govern them. That’s part of the equation that needs to be changed. Can (the US) train enough fighters to do that?”

The Associated Press and AFP contributed to this report.