The Syrian Observatory for Human Rights, a Britain-based monitoring group, said Israel carried out the attacks but gave no further details on its information.
An official from a regional alliance that includes Iran, Syria and Hezbollah confirmed that the strikes near Hama had hit a storage facility on the base and said they had destroyed 200 missiles and killed 16 people, including 11 Iranians.
It said at least one of the attacks hit an arms depot for surface-to-surface missiles at a base in northern Syria known as Brigade 47.
Israel has repeatedly warned that it will not tolerate Iranian military presence in Syria.
Both Iranian and Israeli sources have predicted a retaliation to the strike on Sunday, but before any such answer could be made, Israel dropped a massive cache of dirt on Iran.
He also called on Iranian officials to act wisely in response to the developments in Syria and avoid giving an excuse to Israel for creating tension between the sides in Syria. According to a report in the Al Akhbar newspaper, identified with Hezbollah, bunker buster missiles, which do not explode on impact but rather deep in the ground, hit bases in the Hama and Aleppo areas. "After the attack on Syria attributed to Israel on Sunday night, at least the fifth since September, there seems to be little room for doubt".
He also assured that the failure of the recent aggression against Syria demonstrates the strength of the axis of the resistance, which fights terrorism.
Israel has watched anxiously as Iran first shored up Syrian President Bashar Assad's rule with weapons and money, then committed troops of its own and built military infrastructure across the country.
"These are mixed bases for Iran and regime forces inside Syria, Iranian forces are spread out throughout the country".
The Syrian regime and ally Iran have stepped up attacks on besieged parts of Homs, including the Hola district, even though the region falls within a network of de-escalation zones in which acts of aggression are expressly prohibited.
However, SANA state news agency reported continued intensive bombardment of al-Hajar al-Aswad, another area in the south Damascus pocket where Islamic State militants are based.
The United States, Jordan and Assad's main ally Russian Federation have declared a ceasefire zone in southwest Syria, near the border with Israel, and on Monday Secretary of State Mike Pompeo said Washington's strategy there "remains unchanged".
State news agency SANA said the villages were held by the US -backed Syrian Democratic Forces, adding that they are close to the provincial capital, also called Deir el-Zour.