Jahane Sanat had published an interview with an epidemiologist who said Iran's official COVID-19 figures account for only 5% of the real toll.
Iranian officials had downplayed the fire, which could set back the country's development of advanced centrifuge models.
The Natanz nuclear site is one of the most-tightly guarded sites in all of Iran.
Tehran accuses Trump and 35 others of involvement in the January drone strike that killed Gen. Qassem Soleimani in Baghdad.
The country has reportedly unveiled what experts described as a secret space program with a surprise launch.
Nearly 300 people have been killed and more than 1,000 sickened by ingesting methanol in the mistaken belief it protects against the new coronavirus.
Roughly nine out of 10 of the over 18,000 cases of the new virus confirmed across the Middle East come from Iran.
The Saudi decision expands a ban last week on foreigners visiting Mecca and Medina, home to the holiest sites in Islam.
There are 2,336 cases of the new coronavirus in Iran, including a top emergency official and at least 23 members of parliament.
Mohammad Mirmohammadi became the first top official to succumb to the illness that is affecting members of the Islamic Republic’s leadership.