"They are currently in prison. Their relations are cut off from outside and they are going to be tried," Kharrazi told Reuters on Friday at the World Economic Forum in Davos, Switzerland.
The United States has long accused Tehran of harbouring al-Qaida fighters who escaped Afghanistan after Washington invaded in late 2001 in the wake of the 11 September attacks.
It was the first time that Iran had said it would put suspects of Usama bin Ladin's network on trial.
The most important al-Qaida figure that Western intelligence agencies say may be in Iran is an Egyptian - Saif al-Adil, the network's security chief.
Kharrazi declined to comment on whether Iran was holding al-Adil, saying he could not name any of the suspects for security reasons. Asked if they were important figures, he said: "Al-Qaida members are very important to everyone these days because of operating in different places."
Saudi sources said last year that Iran had also detained Said bin Ladin, a son of Usama, as well as al-Qaida spokesman Sulaiman Abu Ghaith, who is a Kuwaiti, and Jordanian Abu Musab Zarqawi.
The latter has suspected al-Qaida ties and is accused of plotting the murder of a US diplomat in Amman in 2002.
Zarqawi, also named by the Saudi sources as being in Iran, attracted attention when Washington named him in the run-up to war in Iraq last year as a possible link between al-Qaida and Iraqi then-President Saddam Hussein.
Abu Musab Zarqawi is believed
to have been detained by Iran
Washington has said al-Qaida fighters based in Iran plotted suicide bombings in Saudi Arabia last May and has demanded Iran help bring them to justice. Iran denies al-Qaida operated from its territory.
Responding to Tehran's announcements, the White House expressed skepticism on Friday about any attempt by Iran to prosecute al-Qaida members.
Spokesman Scott McClellan said Iran had spurned requests from "a number of countries" to turn over followers of Usama bin Ladin for trial.
"We want to see action, and the action we want to see is that they turn them over to their country of origin," McClellan told reporters. "Any al-Qaida member they have in custody they need to turn over to their home country."