It said activists linked to the students' branch of the basij, Iran's Islamist volunteer militia, distributed the leaflets outside the Jamkaran mosque near the city in central Iran when several pilgrims stepped in to oppose their action.
"Have you come here for the celebration of the 12th imam or are you after your own and your group's interests?" an unnamed pilgrim was quoted as saying.
"We're here for pilgrimage, and even here you're not leaving us alone? Why are you abusing people's religious feelings?”
The mosque is built on the site where the revered missing 12th imam of Shia Islam, Imam Mahdi, is to reappear according to the faith. Every week thousands of pilgrims visit to pay homage there.
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The interior ministry this week banned people from holding gatherings when nuclear negotiations with world powers were taking place, citing security concerns.
"At a time when the negotiating team is busy negotiating, some moves such as holding rallies, whether in favour or against the nuclear negotiations, would damage national security," said interior ministry spokesman Hossein Ali-Amiri, quoted by the KhabarOnline news website.
"The truth is that everyone agrees with the principle of negotiations and everyone wants to reach a result while observing the leader's red lines," he said, referring to Iran's supreme guide, Ayatollah Ali Khamenei.
Tehran and world powers face a June 30 deadline to try to end a 12-year standoff over Iran's controversial nuclear programme and put an atomic bomb beyond the reach of the Islamic republic.
Ultra-conservatives in Iran accuse its negotiators of making too many concessions to the so-called P5+1 of Britain, China, France, Russia, the United States and Germany.