The human rights group said satellite images, video footage and witness accounts showed where dozens of people allegedly killed by Burundian security forces in December were later buried.
"The imagery, dating from late December and early January, shows disturbed earth consistent with witness accounts," it said.
"Witnesses told Amnesty International that the graves were dug on the afternoon of 11 December, in the immediate aftermath of the bloodiest day of Burundi's escalating crisis."
The graves are said to be in the Buringa area, on the outskirts of the capital Bujumbura.
Earlier this month, UN human rights chief Zeid Raad al Hussein called for an urgent investigation into the allegations - which were dismissed by Burundi's government.
He said the increasing number of enforced disappearances, coupled with allegations of secret detention facilities and mass graves was "extremely alarming".
The East African country has been in turmoil since President Pierre Nkurunziza's decision to seek re-election to a third term last April.
There have been mass protests against his government since - including a failed coup in May and a rebellion that has left the country on the brink of civil war.
The Burundian government has also warned any move to deploy African Union peacekeepers to the country will be treated as an invasion.
Briton Philip Edward Moore and his colleague French journalist Jean-Philippe Remy, Africa bureau chief for French daily Le Monde, were among 17 people held.
The paper demanded their immediate release - and on Friday, the Foreign Correspondents' Association of East Africa confirmed they had been freed.
"This is a big relief of course, but the incident bodes ill for our work in Burundi," the FCAEA added in a statement.
Mr Moore and Mr Remy were arrested during a raid on Thursday in Nyakabiga, an anti-government hotspot, as they reported on opponents of Mr Nkurunziza's regime.
"The two foreigners were arrested in the company of armed criminals," the security ministry said in a statement.
Police said a mortar, a Kalashnikov rifle and pistols were also seized during the raid.
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