It was the first time Israel had accused the embattled Syrian leader of using his stockpile of nonconventional weapons.
The assessment, based on visual evidence, could raise pressure on the U.S. and other Western countries to intervene in Syria. Britain and France recently announced that they had evidence that Assad's government had used chemical weapons.
President Barack Obama has warned that the use of chemical weapons by Assad would be a "game changer" and has hinted that it could draw intervention.
But White House spokesman Jay Carney said while the administration is continuing to monitor and investigate whether the Syrian regime has used chemical weapons, it has "not come to the conclusion that there has been that use."
"But it is something that is of great concern to us, to our partners, and obviously unacceptable as the president made clear," Carney said.
Despite the deteriorating situation, NATO officials say there is virtually no chance the alliance will intervene in the civil war. More than 70,000 people have died in the conflict, according to the United Nations. The violence also has forced more than 1 million Syrians to seek safety abroad, and more are leaving by the day, burdening neighboring countries such as Lebanon, Jordan, Turkey and Iraq.
On Tuesday, Brig. Gen. Itai Brun, the head of research and analysis in Israeli military intelligence, told a security conference in Tel Aviv that Assad had used chemical weapons multiple times. Among the incidents were attacks documented by the French and British near Damascus last month.
He cited images of people hurt, but gave no indication he had other evidence, such as soil samples, typically used to verify chemical weapons use.
"To the best of our professional understanding, the regime used lethal chemical weapons against the militants in a series of incidents over the past months, including the relatively famous incident of March 19," Brun said. "Shrunken pupils, foaming at the mouth and other signs indicate, in our view, that lethal chemical weapons were used."
He said sarin, a lethal nerve agent, was probably used. He also said the Syrian regime was using less lethal chemical weapons. And he appeared to lament the lack of response by the international community.
"The fact that chemical weapons were used without an appropriate response is a very disturbing development because it could signal that such a thing is legitimate," he said.
Israel, which borders Syria, has been warily watching the Syrian civil war since fighting erupted there in March 2011. Although Assad is a bitter enemy, Israel has been careful not to take sides, partly because the Assad family has kept the border with Israel quiet for 40 years and partly because of fears of what might happen if he were toppled.
Israeli officials are concerned that Assad's stockpile of chemical weapons and other advanced arms could reach the hands of his ally, the Hezbollah militant group in Lebanon, or Islamic extremist groups trying to oust him from Syria.
Kerry, attending his first meeting of NATO's governing body, the North Atlantic Council, as America's top diplomat, said contingency plans should be put in place to guard against the threat of a chemical strike. Turkey, a member of the military alliance, borders Syria and would be most at risk from such an attack. NATO has already deployed Patriot missile batteries in Turkey.
"Planning regarding Syria, such as what (NATO) has already done, is an appropriate undertaking for the alliance," Kerry told NATO foreign ministers. "We should also carefully and collectively consider how NATO is prepared to respond to protect its members from a Syrian threat, including any potential chemical weapons threat."
Speaking at a news conference after the meeting, NATO Secretary General Anders Fogh Rasmussen said the alliance is "extremely concerned about the use of ballistic missiles in Syria and the possible use of chemical weapons." However, he also noted that NATO has not been asked to intervene.
"There is no call for NATO to play a role, but if these challenges remain unaddressed they could directly affect our own security," he told reporters. "So we will continue to remain extremely vigilant."
Russian Foreign Minister Sergey Lavrov, in Brussels to talk with his counterparts from NATO countries, said Russia would want any investigation of whether chemical weapons have been used to be conducted by experts and concern only the specific report being investigated.
Speaking through a translator in a press conference at NATO headquarters in Brussels, Lavrov said that, in March, after each side in Syria's civil war accused the other of using chemical weapons in northern Aleppo province, the U.N. investigation became politicized and overly broad. Instead of sending experts to study the specific area and the specific allegation, Lavrov said investigators demanded access to all facilities in the country and the right to interview all Syrian citizens.
In Washington, Pentagon spokesman George Little said the U.S. "continues to assess reports of chemical weapons use in Syria."
"The use of such weapons would be entirely unacceptable," he added.
Later in the day, Kerry appeared to try to soften his earlier remarks, saying he had no way of knowing what the facts were.
"I didn't ask for additional planning," he said. "I think it might have been the secretary general or somebody who commented that we may need to do some additional planning. But there is no specific request. What there was from me was a very clear statement about the threat of chemical weapons and the potential for chemical weapons generically to fall into bad hands."
He also said the Obama administration is "looking at every option that could possibly end the violence and usher in a political transition" and that plans need to be made now to ensure that there is no power vacuum when that takes place. He said increasing aid to the Syrian National Coalition and its military command, the Supreme Military Council, would be critical to that effort.
Many of NATO's 28 members also belong to the European Union, which on Monday lifted its oil embargo on Syria to provide more economic support to the rebels and is now considering easing an arms embargo on the country to allow weapons transfers to those fighting the Assad regime.
Kerry did not mention the possible easing of the EU embargo but he did say that NATO should begin to think about taking on a larger role in planning for a post-Assad Syria, particularly in dealing with the country's chemical weapons stockpiles.
The NATO ministers were also working Tuesday on defining how the alliance would support Afghan forces after 2014, when NATO will no longer have a combat role.
With next year's transition date looming, Kerry will host three-way talks in Brussels on Wednesday with Afghan President Hamid Karzai and top Pakistani officials aimed at speeding possible reconciliation talks with the Taliban and improving trust and cooperation between Afghanistan and Pakistan.
On the sidelines of the NATO meeting, Kerry met Lavrov to discuss a range of issues, including Syria. He also thanked Lavrov for Russian President Vladimir Putin's statement of condolence to the U.S. for last week's bombings at the Boston Marathon blamed on two ethnic Chechen brothers.
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