The US has begun reconnaissance flights over Syria in preparation for a possible cross-border expansion of its aerial campaign against Islamic State militants in Iraq.

The flights, involving both manned aircraft and drones, began on Tuesday, an official confirmed to AP, after they were approved by the US president, Barack Obama, over the weekend.

Obama has been reluctant to take military action in Syria, but the flights are being seen as laying the groundwork for extending US air strikes against Islamic State militants (Isis) into the group's stronghold of Raqqa in north-eastern Syria, where it has been leading the fight against the regime of Bashar al-Assad in a civil war that has killed almost 200,000 people.

On Tuesday, Obama warned that defeating Isis would not be easy, but he vowed to pursue the killers of American journalist James Foley.

"America does not forget, our reach is long, we are patient, justice will be done," Obama told veterans gathered at a convention of the American Legion in Charlotte, North Carolina. "Rooting out a cancer like ISIL won't be easy and it won't be quick," he said,

Up to 150 US intelligence operatives have been sent to Baghdad over the past nine months in response to the growing threat posed by Isis, Iraqi officials have told the Guardian. Almost all of the US operatives are connected to the National Security Agency (NSA) and have been tasked with monitoring the phone calls and email traffic of jihadist networks.

Most of the officials arrived early this year, soon after the insurgents seized Fallujah and Ramadi, two Sunni cities west of Baghdad that throughout the US occupation were both strongholds of the Sunni-led insurgency.

Sources in Iraq and elsewhere in the region say the US presence had helped Iraqi forces target Isis militants with airstrikes in western Anbar province in late December. But the intelligence-gathering effort has also extended into Syria, where Isis maintained a command and control centre in the eastern city of Raqaa until mid-June.

Isis has proven to be disciplined in its communications, with senior leaders completely avoiding telephones, email, or anything that the most powerful signals intelligence networks in the world could intercept. Even rare correspondence from the jihadists has proven difficult to track, with the senders using software to hide their tracks.

The White House refused to publicly discuss reconnaissance flights, but did not deny the reports. Spokesman Josh Earnest said the US was willing to take military action to protect US citizens "without regard to international boundaries".

He added: "We are not interested in trying to help the Assad regime," but acknowledged that "there are a lot of cross-pressures here".

Britain's foreign secretary, Philip Hammond, took a similar line last week in the wake of the murder of the American journalist James Foley. He said: "We may very well find that we are fighting, on some occasions, the same people that [Assad] is but that doesn't make us his ally. It would not be practical, sensible or helpful to even think about going down that route."

The irony that the US only a year ago considered – but ultimately rejected – conducting air strikes against Syrian government forces was not lost on the regime.

Assad's foreign minister, Walid al-Muallem, highlighted the possible shifting of international alliances in the region by offering Syrian cooperation in the fight against Isis. But he warned the US against carrying out air strikes on its territory without consent from Damascus. "Any strike which is not coordinated will be considered as aggression," he said.

Muallem revelled in the awkward position the west now finds itself in on Syria, claiming Damascus had repeatedly warned of the nature of the opposition to the Assad government but "no one listened to us".

He condemned Foley's killing in the "strongest possible terms" but asked: "Has the west ever condemned the massacres by the Islamic State againt our armed forces or citizens?"

Officials told the New York Times that the US had not consulted Damascus about the surveillance flights. On Monday, Obama held a meeting with his military commanders and his defence secretary, Chuck Hagel, to discuss the possibility of expanding the US's campaign against Isis, which began with air strikes in Iraq on 8 August.

General Martin Dempsey, the chairman of the joint chiefs of staff, has already conceded the fight against Isis will need to be extended across the border.

"Can they be defeated without addressing that part of their organisation which resides in Syria? The answer is no," he said last week. "That will have to be addressed on both sides of what is essentially at this point a nonexistent border."

Former state department Middle East analyst Aaron David Miller said the Obama administration appeared to have accepted Assad was going to survive in Syria, even as it considered providing military help to moderate opponents of his regime.

Writing in Foreign Policy magazine, he saids: "The battlefield will be expanded; air strikes in Syria will happen. Does it all lack for strategy? Is it a prescription for mission creep? Yes and yes. But blowing up a bunch of very bad people feels good. And whether you approve or not, it's coming."