Iran has said more than 1,000 members of al-Qaeda have been apprehended in the country since the Taleban regime collapsed in Afghanistan in 2001.
Intelligence Minister Ali Younessi says most had been jailed or deported. Some 200 suspects remained in custody.
Iran has always denied US allegations of harbouring senior al-Qaeda members, but it has also been reluctant to give details of arrests in the past.
This is the highest number of suspects Iran has said have been on its soil.
The announcement came before talks with an Iraqi delegation expected to cover security along the Iran-Iraq border.
Mr Younessi said the suspects had come into Iran in five waves, the most recent being last week.
He also said the Iranian authorities had found al-Qaeda terrorist cells in the east of the country in recent days with the help of Sunni clergymen.
Last month, a senior cleric said Iran had arrested and deported nearly 500 al-Qaeda members who had been hiding in the country over the last three years.
Mr Younessi, quoted by the AFP news agency, said Iran was first subjected to an influx of "several thousand Afghans and other nationals" who came into the country illegally after the fall of the Taleban regime, and who were later sent back out.
Then, some al-Qaeda operatives who had taken refuge in Iranian cities were arrested "because they intended to use Iranian territory to launch terrorist strikes on other countries," he said.
"The third wave of al-Qaeda was operating mainly under the cover of Ansar al-Islam, which is based in Iraq. We arrested and tried a number of this group's militants, who are still in prison," he said.
Al-Qaeda members were then linked to a criminal and drug-trafficking gang planning attacks in Tehran and other large cities, he said.
"These elements were also arrested and imprisoned," he said, adding that their chief was still at large.
"Some of the cells we identified act autonomously without being linked to a central command because today al-Qaeda is disorganised," he said.