The anti-Taleban barbs found targets closer to home
He spoke out after hardline Iranian clerics used Friday prayers in Tehran to commend the Afghan movement's use of harsh Islamic punishments.
Mr Khatami, whose country has at times been close to military conflict with Kabul over its treatment of Afghanistan's Shi'a Muslim minority, said the Taleban discredited his religion.
At the same time, he threw the accusation of being un-Islamic back in the faces of Iran's own hardliners and condemned the arrest of a prominent film-maker for allegedly plotting against the Islamic state.
"We do not want Taleban-style security," he told a news conference in the Iranian capital.
"In fact, we consider the Taleban's behaviour and school of thought as a blow to the image of Islam."
Open attack
For Mr Khatami, nothing less than Iran's Islamic Revolution was at stake: "The status of our revolution as a model, as well as our efforts to portray an acceptable image of Islam to the world, may be undermined."
His remarks are therefore all the more significant.
Mr Khatami was crossing swords directly with Ayatollah Jannati, the head of Iran's powerful Council of Guardians, a highly conservative watchdog body.
At Friday prayers, Ayatollah Jannati and another hardline cleric, the former intelligence minister, Ghorban Ali Dorrie Najafabadi, had praised the Taleban for using strict Islamic punishments to keep public order.
For Mr Khatami, to admire the Taleban was tantamount to "insulting the late Imam" - a reference to Ayatollah Khomeini, the leader of the 1979 Islamic Revolution.
On the particular issue of public floggings, which have shocked many Iranians, Mr Khatami said the key question was the interests of the state and society, rather than blind adherence to Islamic prescriptions.
Iranian courts have increased their use of public floggings to fight crimes such as drinking alcohol and harassing women.
But the president promised that the judiciary would soon be circulating instructions which would separate minor offences from more serious ones which might merit such public punishments.
Film director defended
Mr Khatami also expressed regret at the recent arrest of the well-known Iranian film director, Tahmineh Milani.
The judiciary said she had been arrested in connection with her latest film, The Hidden Half, which has been showing in Tehran for the past month.
Mr Khatami said it was unfair that a director should be arrested for a film which had received government permission, as all films must do.
The intelligence ministry had no record of Mrs Milani being involved with subversive organisations, Mr Khatami said.
Without referring to anyone specifically, he also commented that works of art should not be "dealt with on the basis of personal views and preferences".