The arrests came after clashes between police and ethnic Arabs, who are seeking independence, in the provincial capital of Ahwaz.
Several state buildings, including banks, and police cars were damaged and at least three people were injured, according to the official Islamic Republic News Agency (Irna).
"Many of those arrested are young, innocent people. The real criminals are those who provoked them," Intelligence Minister Ali Yunesi was quoted as saying by Irna in Tehran on Monday.
"We have arrested many of those behind the scenes and it became evident that they have ties to anti-government channels," he added.
It was not clear which television channels Yunesi was referring to.
Broadcast media in Iran is in the hands of the state, but many Iranians tune in to foreign channels via illegal satellite dishes.
At least one person died after Arab-Iranians went on the rampage in Khuzestan province bordering Iraq on Friday and Saturday.
Government officials have said the violence in Iran's traditional oil-producing heartland was sparked by a forged letter, supposedly penned by a senior government official, discussing the idea of relocating ethnic Arabs from the area. Iran dismissed the letter as forged.
One exile opposition group campaigning for Khuzestan's independence from non-Arab Iran, the London-based Ahvaz Arab People Democratic-Popular Front, said the violence was far worse than official accounts, and put the toll much higher.
But officials said peace and order had been restored to the area by Sunday, and there were no other reports of renewed violence.
Arabs make up about 3% of Iran's 67 million population and most of them live in the southwest of the country.