The organisation, headquartered in London, will shed five of its seven-strong senior management team after the review into "staff wellbeing" ordered last year by secretary-general Kumi Naidoo.
It found working at Amnesty often put employees under "exceptional stress" and that its efforts to support staff had been "ad hoc, reactive and piecemeal".
"Amnesty as a working environment is often described as 'toxic'," the report, carried out by consultants The KonTerra Group, stated.
"Organisational culture and management failures are the root cause of most staff wellbeing issues," it concluded.
Amnesty initiated the probe last August after Gaetan Mootoo, a well-known researcher, and paid intern Roz McGregor took their own lives within three months of each other that year.
Mootoo, who had been with the organisation for decades and was known across Africa for his tireless dedication to his work, killed himself in its Paris offices where he worked.
The 65-year-old left a suicide note allegedly "outlining his previous request for help because of the heavy and additional workload; help which was never forthcoming".
McGregor, 28, a British intern working at Amnesty's Geneva office, reportedly suffered from insomnia and anxiety, and committed suicide at her family's home near London six weeks after Mootoo's death.
The human rights champion conceded the review painted "a somber picture" of its own recent internal track record, following its release in January.
"To hear our employees speak of a culture of secrecy and mistrust where discrimination, bullying and abuse of power have been condoned is profoundly troubling," Naidoo said in a statement.
The secretary-general unveiled his management restructuring at a meeting on May 9, with the departing directors set to have left by October, according to Amnesty.
A new "coalition leadership team" will become operational in November with just four directors.
The Times reported there was anger within Amnesty that the managers leaving would receive "generous" redundancy payments -- in contrast to scores of other staff laid off due to a funding crisis.
However an Amnesty spokesperson said the directors' terms were "less favourable than that of other staff".