"The intelligence ministry is in charge of investigating accusations against Hossein Moussavian," the official IRNA news agency quoted Saeed Mortazavi as saying.
He confirmed that Moussavian was in custody but refused to specify the allegations against him "until the investigations are complete."
The semi-official Fars news agency said on Wednesday that Moussavian "was arrested and detained for a series of links with foreigners and exchanging information with them."
Quoting unnamed sources it said "Moussavian had probably exchanged information with foreigners over nuclear issues and he could face espionage charges."
He played a central role in talks that saw Iran strike a deal with Europe under which it suspended its controversial uranium enrichment activities, a freeze which was reversed when President Mahmoud Ahmadinejad came to power.
The nuclear negotiating team under Khatami was considered close to the centrist cleric and former president Akbar Hashemi Rafsanjani, who was thrashed by Ahmadinejad in 2005 presidential elections.