The organization revealed its count that included regime opponents, Baha'is and other religious minorities and at least 860 journalists.
The group said at a news conference that its information was based on a confidential file of judicial proceedings obtained by whistleblowers.
The file registering judicial procedures contains details on some 1.7 million people, including minors, locked up in Evin prison in the first three decades of the Islamic regime that overthrew Shah Mohammad Reza Pahlavi, shaking the region and the world.
Among the journalists, at least four were executed, according to RSF, as the watchdog group is known. The organization noted that the detailed Iranian file never mentions the professional status of individuals, suggesting this made it easier for the regime to claim it wasn't holding journalists or, more broadly, prisoners of conscience.
RSF set up a committee that combed through the Iranian file. It is headed by 2003 Nobel Peace Prize Laureate Shirin Ebadi, an Iranian human rights lawyer.
The file reveals some previously undisclosed information, RSF said,
"After months of verification, we have identified in these files of 1.7 million records, the cases of at least 61,940 political prisoners during the period of 1979 until 2009, only in Tehran," said Christophe Deloire, head of RSF.
Of these, 520 were aged between 15 and 18, he said.
Deloire said the files show the "relentless machinations" used "to persecute men and women for their opinions or their reporting."
RSF is referring "these state lies" to the U.N. human rights commissioner, Michelle Bachelet, "so that Iran can be held to account," he said.