Even though the White House has all but ruled out military intervention, the Pentagon is drafting contingency plans for operations with NATO or regional allies to manage a large flow of refugees over Syria’s borders and safeguard the country’s arsenal of chemical weapons…

The State Department effort is being coordinated by Deputy Secretary of State William J. Burns, who worked in the Near Eastern Affairs Bureau during the planning for the American invasion of Iraq in 2003, when the department clashed with the Pentagon over what to do after Mr. Hussein’s fall. The department has created a number of separate cells devoted to aspects of a post-Assad Syria, including humanitarian issues, economic reconstruction, security, the stockpiles of chemical weapons and a political transition…

The range of plans being drafted, however, underscored the gravity of the risks. Atop the list is protecting Syria’s chemical weapons, which its leaders acknowledged possessing when vowing last month to use them only in the event of a foreign invasion. “That would be a purely military-type mission, and so we have to think about contingency planning for safeguarding these stockpiles,” one official said.

The Pentagon has also offered Jordan and Turkey assistance in defending their borders and managing the influx of refugees, as well as ensuring the delivery of humanitarian supplies. Defense Secretary Leon E. Panetta discussed these issues with King Abdullah II of Jordan in Amman on Thursday, said the Pentagon’s press secretary, George Little, who declined to discuss specific contingency planning.