Ahmadinejad last week caused controversy when he described the airborne attacks on New York and Washington by Al-Qaeda militants as a "suspect event" and cast doubt on the strikes in three speeches within the space of eight days.
"Regarding 9/11, as long as all the aspects have not been clarified this remains a suspicious incident," foreign ministry spokesman Mohammad Ali Hosseini told reporters.
"Many analysts and observers who have followed this feel that there are many suspicions and ambiguities. There are many points of ambiguity surrounding it," he added.
US State Department spokesman Sean McCormack said he had been left "speechless" by Ahmadinejad's comments which he condemned as "misguided, misinformed rhetoric."
Ahmadinejad expressed suspicion that the names of the dead from the attacks "were never published" even though the names of more than 2,700 victims have been read out at annual memorial ceremonies.
He also said the United States used the strikes a "pretext" to launch invasions of Iraq and Afghanistan.
The controversial president has previously provoked outrage by describing the Holocaust as a myth and raising doubts over the scale of the mass slaughter of Jews in World War II.
