WASHINGTON — President Obama has authorized surveillance flights over Syria, a precursor to potential airstrikes there, but a mounting concern for the White House is how to target the Sunni extremists without helping President Bashar Assad.

Defense officials said Monday evening the Pentagon is sending in manned and unmanned reconnaissance flights over Syria, using a combination of aircraft, including drones and possibly U-2 spy planes. Obama approved the flights over the weekend, a senior administration official said.

The flights are a significant step toward direct U.S. military action in Syria, an intervention that could alter the battlefield in the nation’s three-year civil war.

Administration officials said the United States had no plans to notify the Assad government of the planned flights. Obama, who has repeatedly called for the ouster of Assad, is loath to be seen as aiding the Syrian government, even inadvertently.

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As a result the Pentagon is drafting military options that would strike the militant Islamic State near the largely erased border between those two nations, as opposed to more deeply inside Syria.

The administration is also moving to bolster U.S. support for the moderate Syrian rebels who view Assad as their main foe.

On Monday, Syria warned the U.S. that it needed to coordinate airstrikes against the Islamic State or it would view them as a breach of its sovereignty and an “act of aggression.” But it signaled its readiness to work with the United States in a coordinated campaign against the militants.

The reconnaissance flights would not be the first time the United States has entered Syrian air space without seeking permission. In July, U.S. special-operations forces carried out an unsuccessful rescue attempt for hostages held by the Islamic State, including journalist James Foley, whose death was revealed last week in a video.

The White House press secretary made clear that if the president did act, he had no plans to collaborate with Assad or even inform him in advance of any operation.

“It is not the case that the enemy of my enemy is my friend,” said Benjamin J. Rhodes, a deputy national security adviser. “Joining forces with Assad would essentially permanently alienate the Sunni population in both Syria and Iraq, who are necessary to dislodging ISIL,” he said, using an alternative name for the group, the Islamic State in Iraq and the Levant.

Still, administration officials acknowledge that the sudden threat from the Islamic State to Americans — several of whom are still held by the militants in Syria — had complicated the calculus for the U.S. in a conflict Obama has largely avoided.

Under plans being developed by the administration, a senior official said, the U.S. could target leaders of the militant group in and around their stronghold, the northern city of Raqqa, as well as in isolated outposts to the east, near the Iraqi border.

While the Syrian government has the capability to partly defend its airspace from U.S. warplanes, American fighter jets can fly close to the border and fire on targets in Syria using long-range precision weapons.

The U.S. military could also jam Syria’s air-defense systems by sending signals that would make it difficult or impossible for radar to pick up U.S. fighter planes entering Syrian airspace. Such a move would give fighters a limited amount of time to hit Islamic State targets or camps before exiting Syria.

The military could also use B-2 stealth bombers, which are almost invisible to radar, or could fire at stationary targets in Syria using Tomahawk cruise missiles, launched from ships at sea.

On Monday, even as he warned the Obama administration against unilateral strikes in Syria, Walid Muallem, the Syrian foreign minister, said, “Syria is ready for cooperation and coordination at the regional and international level to fight terrorism.”

Syria’s strategy, say some former administration officials, carries a risk for the United States, particularly if the moderate opposition is squeezed out by the Islamic State.

“We’re going to find ourselves maneuvered into a very uncomfortable position,” said Frederic C. Hof, a former State Department official who worked on Syria policy. “We’re unconsciously walking into an ambush.”