Iran said the groups had encouraged post-election violence
Iran has banned its citizens from co-operating with foreign organisations it says are trying to destabilise the government, state media has reported.
The 60 blacklisted groups include human rights groups, Iranian opposition websites and media groups such as the BBC and US broadcasters.
Iran's deputy intelligence minister told Press TV the groups were involved in a "soft war" against the state.
The official said the groups had helped incite post-election unrest.
The BBC, Voice of America, the US National Defense University, the Soros Foundation, Human Rights Watch (HRW) and the East European Democratic Centre (EEDC) were among the organisations named.
Tehran has issues similar bans in the past and the terms of the ban itself remain unclear.
But Press TV quoted the official as saying that co-operating with the groups, signing contracts with them or receiving assistance from them was illegal.
He said it was also illegal for foreign parties to receive funding from foreign countries and warned citizens to avoid "any unusual relations" with foreign embassies and nationals.
Iran says several foreigners and Iranians with dual nationality were among those detained during anti-government demonstrations at the end of December.
RECENT UNREST IN IRAN
19 Dec: Influential dissident cleric Grand Ayatollah Hoseyn Ali Montazeri dies aged 87
21 Dec: Tens of thousands attend his funeral in Qom; reports of clashes between opposition supporters and security forces
22 Dec: Further confrontations reported in Qom
23 Dec: More clashes reported in city of Isfahan as memorial is held
24 Dec: Iran reportedly bans further memorial services for Montazeri except in his birthplace and Qom
26 Dec: Clashes reported in central and northern Tehran
27 Dec: At least eight dead following anti-government protests in Tehran; 300 reported arrested
At a news conference on Tuesday, Foreign Ministry spokesman Ramin Mehmanparast said action would also be taken against those arrested if they were found to have been leading what he called a "psychological war" against the government.
"Naturally their legal and judicial process is under way," he said.
"Those who did not demonstrate any crime will be released and those who committed a crime will be confronted if their crime is demonstrated."
Also on Tuesday, Tehran announced it had postponed a visit by Euro MPs who were planning to meet Iranian opposition activists and Majlis (parliament) members in the capital this week.
Iran said a new date would set "by mutual agreement" but the head of the EU delegation accused Tehran of trying to avoid drawing attention to recent political unrest.
The protests, which began after President Mahmoud Ahmadinejad's controversial re-election in June, have grown into the biggest challenge to the government since the 1979 Islamic revolution.