In a case that underscores the gulf between Iranian moderates, who seek fewer Internet restrictions, and conservatives who want more, the Silicon Valley leader has been dubbed the "Zionist manager" of Facebook, on account of his Jewish heritage.
The court in Fars province ordered that Zuckerberg address unspecified "violation of privacy" claims made by Iranians over the reach of Facebook-owned apps, ISNA news agency reported.
Access to social networks, including Twitter and Facebook, are routinely blocked by Iranian authorities, as are other websites considered un-Islamic or detrimental to the regime.
"Following a complaint lodged by some of our fellow countrymen over the violation of their privacy and problems ensuing from WhatsApp and Instagram, the judiciary official has ordered a ban on these two software devices," he said.
Facebook owns Instagram and WhatsApp.
The report did not say what violations of privacy are alleged to have occurred.
President Hassan Rouhani, a self-declared moderate, has promised greater tolerance on social, cultural and media issues -- a vow that helped him defeat conservatives in last year's election.
Officials have voiced support for lifting the wider ban on social media, with some of them having Facebook or Twitter accounts.
Rouhani earlier this month vetoed a plan to ban WhatsApp, preventing implementation of curbs sought by Iran's Committee for Determining Criminal Web Content.
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