The Israeli army on Tuesday said Damascus had used chemical weapons as US Defence Secretary Chuck Hagel wrapped up a three-day visit to Israel focused on the Syrian civil war and the Iranian nuclear threat.

The remarks were made by a top official in Israel's military intelligence as Hagel met with Israeli Prime Minister Benjamin Netanyahu shortly before departing for a brief visit to Jordan.

"To the best of our professional understanding, the regime (of Syrian President Bashar al-Assad) has made use of deadly chemical weapons against the rebels in a number of incidents in the last few months," said Brigadier General Itai Brun, head of the research and analysis division of military intelligence.

Speaking to delegates at a Tel Aviv security conference, he cited an incident on March 19 in Aleppo province in which 31 people were killed, pointing to the physical symptoms suffered by those in the area at the time.

"The reduced pupils, the foam coming out of the mouth and other additional signs provide evidence that deadly chemical weapons have been used," he said, indicating the symptoms were observed in photographs taken of the affected area.

"Which chemical weapons? Apparently sarin. The regime is also using chemical weapons that neutralise and are not fatal," he added.

Developed as a pesticide in Germany in 1938, sarin is a deadly and volatile nerve agent that is colourless and odourless.

The United States has said any use of chemical agents would cross a "red line," evoking possible military action.

But Washington could not confirm Israel's account and intelligence agencies were still reviewing the reports.

"The United States continues to assess reports of chemical weapons in Syria," Hagel's spokesman George Little said in a statement.

But he warned the Assad regime against the use of chemical agents or allowing them to fall into the hands of groups like Lebanon's Hezbollah.

"We reiterate in the strongest possible terms the obligations of the Syrian regime to safeguard its chemical weapons stockpiles, and not to use or transfer such weapons to terrorist groups like Hezbollah," he said in Jordan.

The war in Syria was expected to top the agenda in Hagel's talks with Jordanian army chief General Masbal al-Zaben.

Hagel has ordered a US Army headquarters element to Jordan to bolster an American contingent there that is tasked with preparing for possible worst-case scenarios, including securing chemical weapons sites in Syria or a spillover of violence from the conflict.

Speaking shortly before his talks with Hagel, Netanyahu alluded to the Iranian-backed transfer of advanced arms from Syria into militant hands, and stressed that the Jewish state would do whatever it takes to defend itself.

Netanyahu's remarks came a day after Defence Minister Moshe Yaalon implicitly confirmed Israeli involvement in a January strike on a weapons convoy in Syria which was understood to be heading to Hezbollah, saying Israel had "acted" to stop advanced weaponry reaching militants.

The Shiite militia group and the Syrian regime of Assad are both close allies of Iran and avowed enemies of Israel.

Addressing the January 30 strike, the Israeli military intelligence analyst said the target of the strike was Russian-made SA-17 anti-aircraft missiles which were en route to Lebanon's Hezbollah.

"The SA-17 missile launchers that were bombed in Syria were going to be transferred to Hezbollah," Brun said, his remarks published on Haaretz's website.

After his brief stopover in Jordan, Hagel headed to Riyadh and was also scheduled to visit Cairo and Abu Dhabi later in the week.

One of the main objectives of his trip is to put the finishing touches on a multi-billion dollar arms deal which will see the sale of advanced US missiles, radar and aircraft to Israel, missiles to Saudi Arabia and F-16 fighter jets to the United Arab Emirates.