Maj. Gen. Aviv Kochavi, addressing the 13th Annual Herzliya Conference, cautioned that Assad has not yet ordered the use of such weapons, Haaretz reported.
With rebel forces controlling much of the country, Kochavi said Syria should now be viewed as two countries.
He said Hezbollah and Iran have been working with Syrian forces to bring stability to the regime. Hezbollah fighters killed in the fighting have been buried in secret so their identities won't be revealed, Kochavi said.
In other comments, the intelligence chief said Iran does not expect an attack by the international community on its nuclear facilities "in the foreseeable future."
The weight of sanctions could eventually change Iran's decision about the facilities, Kochavi said, but had not yet done so.
The Syrian Network for Human Rights said it documented 105 deaths from violence throughout Syria Thursday, including 19 children and eight women.
The report said 32 people were killed in and around Damascus, the capital, 22 were killed in Homs, 12 in Daraa, nine in Aleppo and seven in Raqqa.
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