The drills -- dubbed Eqtedar, or "might", in Farsi -- have involved the Islamic Revolutionary Guard Corps (IRGC), the ideological branch of Iran's military, alongside the army.
"The first phase of the joint Eqtedar exercises in the air defense zone of the Natanz nuclear facility has commenced under the orders of the air defense headquarters commander," state TV said.
It added that IRGC air forces were undertaking "an all-out point defense" of the site "against a multitude of air threats in tough electronic warfare conditions".
On Monday, IRGC spokesman Ali Mohammad Naini said the drills, which will also cover other parts of Iran until mid-March, were being conducted in response to "new security threats", without elaborating.
Several branches of the IRGC, including the navy and the paramilitary Basij forces, will also take part in the exercises, he added.
Last week, US news website Axios reported that White House national security adviser Jake Sullivan had presented President Joe Biden with options for a potential US strike on Iran's nuclear facilities if Tehran moved toward developing a nuclear weapon before January 20, when Donald Trump takes office.
Iran's foreign ministry spokesman Esmaeil Baqaei lambasted the reports, saying threats against the country's nuclear facilities were "a gross violation of international law".
Iran maintains that its nuclear programme is solely for peaceful purposes and denies any intention to develop atomic weapons.
Iran has in recent years increased its manufacturing of enriched uranium, and it is the only non-nuclear weapons state to possess uranium enriched to 60 percent, the International Atomic Energy Agency (IAEA) nuclear watchdog said.
That level is well on the way to the 90 percent required for an atomic bomb.
Tensions over Iran's nuclear programme soared after the United States, during Trump's first term in office, withdrew from a landmark nuclear deal that offered Tehran sanctions relief in return for curbs on its nuclear ambitions.
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