Iran's Revolutionary Guard Corps' (IRGC) al-Quds Force reportedly operates the base, which is located outside of the Syrian capital of Damascus.
Israel has been warning for years that Iran is seeking to entrench itself militarily in Syria, including establishing missile bases.
A satellite image showing an alleged Iranian base on the outskirts of a Syrian army base outside Damascus.
Israeli defence minister Avigdor Liberman downplayed the report - telling Israel radio there is "nothing new here" and assuring "we have the full picture of what's going on". But recent incident of Israeli air raids on Iranian bases in Syria and downing of Israeli F-16 fighter jet by Syrian antiaircraft missile batteries which has happened for first time in 36 years has bought these two nations into direct confrontation with each other.
The revelations come after General Joseph L. Votel, head of U.S. Central Command, warned Iran has "enhanced" its support of Syria.
Earlier this month, the IDF shot down a drone belonging to Iran that entered Israeli airspace in the Golan Heights.
Prime Minister Benjamin Netanyahu delivers a speech on the third day of the 54th Munich Security Conference (MSC) held at the Bayerischer Hof hotel, in Munich, southern Germany, on February 18, 2018. The outlet, which appears to have well-placed sources in both the opposition and Syrian regime, has reported extensively on Iranian involvement in the country's civil war.
Senator Lindsey Graham said Iran is testing President Donald Trump and warned Israel was preparing to start a war in southern Lebanon over an Iranian-backed Hezbollah rocket factory.
The figures could not be independently confirmed, but Danon said the Iranians 'speak about 100,000 troops under their control in Syria'.
IAF chief Maj. Gen Amikam Norkin said the "thorough investigation that we have carried out shows a learning process at all levels both at headquarters and in the field and will make the air force even better".