The sharp attack by Gen. Mohammad Ali Jafari effectively labels Khatami and others as potential foes of the ruling system and could place them at higher risk of being directly punished by hard-line authorities.
Khatami's former vice president, Mohammad Abtahi, is among more than 100 activists and pro-reform politicians facing trial on charges of plotting against the Islamic regime following the disputed presidential elections in June.
But Khatami and several other opposition leaders — including the election challengers to President Mahmoud Ahmadinejad — have not been detained.
Jafari's accusations could open more room for action against Khatami and others such as Mir Hossein Mousavi, whose backers say was robbed of victory by massive vote fraud. It also pointed to possible new rifts in the establishment about how to deal with the top opposition figures.
Jafari was quoted by the official Islamic Republic News Agency as claiming Khatami and allies encouraged the massive street protests after the vote and tried to undermine the authority of Supreme Leader Ayatollah Ali Khamenei, who holds the pinnacle of power in Iran's theocracy.