Aziz Asber, who ran the Masyaf base near the northern city of Hama, died when his vehicle exploded on Saturday evening.
The unit was said to be developing short-range surface-to-surface missiles with experts present from the Syrian regime's ally, Iran.
Al-Watan reported Sunday morning that "according to assessment Israel was involved in the assassination, as it had carried out several air strikes on the Center for Scientific Research, the last one on July 22".
Syrian President Bashar Assad said in an interview in June with Russia's state-controlled NTV television channel that his government got rid of all its chemical weapons in 2013 and that allegations of their use were a pretext for invasion by other countries.
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The baby boy, thought to be about 8 months old, was transported to a local hospital where he was pronounced dead. No parent or guardian was present at the scene and the child showed no signs of trauma, police said.
As in all similar cases, Israel neither confirmed nor denied the report.
It is unknown who was behind the attack.
The Masyaf facility has previously been hit by what the Syrian government said were Israeli strikes in July and previous year in September.
Missile strikes by the US, Britain and France destroyed another Syrian scientific studies and research centre facility in Damascus in April, in response to a suspected poison gas attack.
Syria has denied owning or using chemical weapons, but the U.S. and the Syrian opposition accuse the government of carrying out a chemical attack on former opposition stronghold Douma near Damascus that reportedly killed 40 people in April this year. Syria agreed to hand over its chemical weapons stockpiles and dismantle production facilities amid worldwide outrage following that attack.