"Since the attack, about 100 people have been arrested, of whom some have been released," Gholamhossein Mohseni Ejeie was quoted as saying by the official IRNA news agency.
The ransacking of the embassy earlier this month "has been condemned by all authorities and we have taken immediate and serious action," he added.
One individual was also arrested "abroad" and returned to Iran, he said.
"He had given orders to certain individuals who entered the embassy," Ejeie added, without providing further details.
Demonstrators stormed and burned Riyadhs embassy in Tehran and its consulate in second city Mashhad on January 2 to protest against the execution of a prominent cleric from Saudi Arabias Shiite minority.
The Gulf kingdom and some of its allies the next day severed diplomatic relations with Iran over the incidents.
The Islamic republics supreme leader Ayatollah Ali Khamenei on Wednesday condemned the attack.
"Like the British embassy attack before it, this was against the country (Iran) and Islam, and I didnt like it," he said, referring to a mob ransacking Britains embassy in Tehran in 2011.
President Hassan Rouhani also condemned the attacks as "totally unjustifiable" and called on the judiciary to put on trial those accused of being involved.
Iran previously said it had arrested 40 people over the embassy attack in Tehran, and another four after the consulate was torched in Mashhad.(*)
Editor: Heru Purwanto
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