Their statement Thursday came a day after the government said it had launched inquiries into the unrest, which it said had claimed 16 lives.
The June 1-3 violence was sparked by a two-year sentence on opposition figurehead Ousmane Sonko for "corrupting" a young woman, making him ineligible to contest presidential polls next year.
Around 23 people died, according to Amnesty's figures "including some by gunfire, have been registered between Dakar and Ziguinchor (in the north)," the organization said. Three of those killed were minors, the statement added.
Sonko's PASTEF-Patriots party put the death toll at 26.
Amnesty said that having examined videos of the violence, it had identified armed men dressed in civilian clothing working alongside the security forces and attacking demonstrators.
The footage was evidence of human rights violations, said Seydi Gassama, Amnesty Senegal's executive director.
Sonko has repeatedly insisted his prosecution and eventual conviction was a ploy by the government to keep him from running for the presidency — a claim the government has denied.
Contacted by AFP, the government did not respond to Amnesty's statement.
Human Rights Watch has criticized authorities' response to the unrest and called for an inquiry.
The Senegalese authorities have banned two opposition marches planned for Friday and Saturday against President Macky Sall, the prefecture told AFP.