Khamenei has already accused the United States, Israel and their "agents" of fomenting the unrest sparked by 22-year-old Kurdish woman Amini's death after her arrest for allegedly wearing her hijab 'incorrectly'.
"Today, everyone confirms the involvement of the enemies in these street riots," Khamenei said on Wednesday in a televised meeting with the Expediency Council, an advisory body.
"The actions of the enemy, such as propaganda, trying to influence minds, creating excitement, encouraging and even teaching the manufacture of incendiary materials, are now completely clear," he said, without identifying the enemy.
Earlier on Wednesday, the judiciary said it had charged more than 100 people over the protests in Tehran and Hormozgan provinces.
"Some of these people are either enemy agents or… aligned with the enemy, and some are excited people," Khamenei said.
"The judicial and security authorities must do their duty" in dealing with the "enemy agents", he said.
Since 16 September, dozens of people – mainly protesters but also members of the security forces – have been killed while hundreds of others have been arrested in several cities across the country.
Amini, whose Kurdish name can be spelt "Jina" or "Zhina", was detained by the morality police in Tehran on 13 September.
The authorities, who have been accused of beating her, maintain that she died from natural causes.