Gen. Salim Idris' departure from Syria is "a big problem" but the United States continues to support him and the moderate opposition, Defense Secretary Chuck Hagel said today.

Idris is the head of the Free Syrian Army who reportedly fled Syria to Qatar this weekend after Islamic fighters took control of his group's headquarters and warehouses in northern Syria stocked with U.S. aid. That seizure prompted an end of U.S non-lethal assistance to rebels in that part of Syria to prevent it from getting into the hands of extremist rebels.

READ: Obama Makes Syria Pitch on Capitol Hill

At a Pentagon news conference today with the visiting defense minister of Singapore, Hagel acknowledged Idris' departure as "a big problem and we're going to have to work through it and manage through it with General Idris and moderate opposition."

Hagel said "we continue to support General Idris and the moderate opposition, and we are going to continue to help in the humanitarian area, which we have been doing consistently."

The Defense secretary said developments in Syria in the past couple days are a "clear reflection on how complicated and dangerous this situation is and how unpredictable it is."

READ: US Prepares to Destroy Syrian Chemical Weapons at Sea

As for the seizing of the Free Syrian Army's warehouses by Islamic fighters, Hagel said assessments about its effects were ongoing. "We're evaluating everything right now," Hagel said. "We're assessing what has happened, where we are. So I would leave it at that."

Overall, he said, Syria "continues to be a very difficult problem," given the wide range of rebel groups, particularly what he called the "dangerous elements" that complicate U.S. support for rebel groups. "It's not a matter of just an easy choice between the good guys and the bad guys here," he added.

Hagel said those dangerous elements prompted the U.S. decision to withhold "the nonlethal assistance in these warehouses and so on until, first of all, we can get a clear assessment of what has happened."

Hagel said the plan to destroy Syria's chemical weapons program is on track, including the possibility that the United States will destroy the most dangerous precursors at sea.