Amnesty's report, released on Thursday, examines allegations of torture, rape, death threats, forced confessions, intimidation, cover-ups and unlawful killings in the period after the country's disputed presidential election in June.
The rights group called on Ayatollah Ali Khamenei, Iran's supreme leader, to allow United Nations human rights experts to visit the country to help carry out an investigation.
Official inquiries to date "seemed to have been more concerned with covering up abuses than getting at the truth", the report said.
Iran has dismissed previous criticism of its human rights record.
"Members of militias and officials who have committed violations must also be promptly held to account and on no account should anyone be executed," Hassiba Hadj Sahraoui, the deputy director of Amnesty International's Middle East and North Africa Programme, said in a statement on Thursday.Official figures say 36 people died in post-election violence, but Iran's opposition says around 70 people died.
More than 4,000 people were arrested after the poll, and around 200 remain in prison.
The report claimed "patterns of abuse" before, during and after the election, when authorities deployed the the Basij militia and Revolutionary Guards to suppress mass protests against its disputed outcome.
Mass demonstrations against the re-election of Mahmoud Ahmadinejad, the Iranian president, plunged the Islamic Republic into crisis.
However, opposition rallies no longer muster the huge crowds that flooded the streets immediately after the June 12 ballot.
Mirhossein Mousavi, a defeated election candidate, has alleged that the vote was rigged.
Some of those detained during the protests have since been forced to flee the country, the report said.
One former detainee says he was held at the Kahrizak detention centre for about 58 days, kept in a shipping container throughout and only allowed to contact his family after 43 days, the report said.
"Anyone who is arrested or detained must be protected from torture or other ill-treatment, prisoners of conscience must be released and those convicted after unfair trials - including the "show trials" which made a mockery of justice - must have their cases reviewed, or be released," Sahraoui said.
"All death sentences should be commuted, and others not yet tried must receive fair trials."