Confirming that Esfandiari was also still being held in Tehran's Evin prison, he said: "The same goes for Mr Tajbakhsh. He is being kept in detention.
"Ms Azima is not detained. She is at liberty but bears the same accusations" as the two detained scholars.
All three suspects have US and Iranian passports but Iran does not recognise dual nationality.
"Iran has a right to pursue nuclear power but it should abide by international agreements and laws"
David, NYC, US
Send us your views
Jamshidi's comments were the first time Iran has confirmed Tajbakhsh's detention or indicated that Azima also faces such serious accusations.
An expert in urban planning who has taught in the US and Iran and worked for the World Bank, Tajbakhsh was according to US press reports arrested on May 11.
He has also worked for the Open Society Institute of George Soros, the US billionaire, that is accused by Iran of seeking a "Velvet Revolution" in Iran similar to the ousting of communism in eastern Europe.Vitriolic attacks
The Washington-based Woodrow Wilson Centre for International Scholars, where Esfandiari works as head of the Middle East programme, has been linked by the Iranian authorities to an "overthrow bid" by the Soros institute.
Both Tajbakhsh and Esfandiari have been the target of vitriolic attacks in Kayhan newspaper, the mouthpiece of Iran's clerical authorities, for allegedly seeking to topple the government.
Esfandiari travelled to Iran in December to visit her 93-year-old ailing mother, but her passport was confiscated and she was subjected to interrogations by intelligence before being arrested on May 8 and sent to Evin prison.
Azima, a journalist for the US-funded Persian arm of Radio Free Europe who was like Esfandiari visiting Iran to call on a sick relative, had her passport confiscated by the authorities and is unable to leave the country.'Not detained'
US media and Human Rights Watch have said that Ali Shakeri, a third US-Iranian, has been detained in Iran in recent weeks but Jamshidi said Shakeri was "not detained", without giving further details.
The announcement of the charges brought by Iran's intelligence ministry against the trio underlined the mutual suspicion that remains between Iran and the US, just a day after the two sides held talks in Baghdad.
The arrests have been condemned by the US State Department, which is also concerned about the fate of Robert Levinson, a US citizen, who it says went missing while visiting Iran's southern resort island of Kish.
Iran has said it has no knowledge Levinson even entering Iran and has vehemently denied US suggestions that he may have been arrested.