The operatives may have provided transit for at least eight of the 19 men who wreaked havoc in the United States with hijacked airliners on 11 September, the commission said in its report released on Thursday.
Al-Qaida and Iranian operatives struck an accord in late 1991 or 1992 to provide training for assaults on Israel and the United States, and "terrorist" leaders and trainers went to Iran for instruction in explosives, the report said.
The commission said that "intelligence indicates the persistence of contacts between Iranian security officials and senior al-Qaida figures" after Usama bin Ladin returned to Afghanistan from Sudan in 1996.
Some 9/11 hijackers transited
through Iran, says commission
It quotes captured "terrorist" leader Walid bin Attash, known as Khallad, as saying Teheran tried to strengthen ties with al-Qaida after the 2000 attack on the USS Cole but was rebuffed by bin Ladin out of concern for Saudi sensitivities.
It also cites captured 11 September planner Ramzi bin Al-Shibh as saying that at least eight hijackers transited Iran en route to and from Afghanistan, "taking advantage of the Iranian practice of not stamping Saudi passports."
The report said circumstantial evidence suggested that senior operatives of the Iranian-supported group Hizb Allah closely tracked the travel of some hijackers into Iran in November 2000. But it said this may just be coincidence.
"We found no evidence that Iran or Hizb Allah was aware of the planning for what later became the 9/11 attack," the panel said.
"It's harder to make the leap that they were directing operations like that"
Unnamed CIA official
"At the time of their travel through Iran, the al-Qaida operatives themselves were probably not aware of the specific details of their future operations."
The panel called for further investigation by the government, which Bush has already promised.
A senior CIA official acknowledged "some murkiness" on Teheran's relationship with al-Qaida but said it was possible that the Iranians had some "operational knowledge" of its activities.
"It's harder to make the leap that they were directing operations like that," said the official, who asked not to be named.