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

As a result the Pentagon is drafting military options that would strike the militant Islamic State in Iraq and Syria, or ISIS, near the largely erased border between those two nations, as opposed to more deeply inside Syria. The administration is also moving to bolster American support for the moderate Syrian rebels who view Mr. Assad as their main foe.

On Monday, Syria warned the White House that it needed to coordinate airstrikes against ISIS 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.