The annual report released on Monday highlights the state of human rights in 156 nations last year.
In Mozambique, Amnesty International says an armed group calling itself al-Shabab continues to behead civilians, abduct women and girls, as well as looting and burning villages.
Tigere Chagutah, Amnesty International's interim regional director for East and southern Africa, told reporters in Johannesburg that the activities of the group have triggered a crisis.
"The situation has not received the attention that it deserves. This is a forgotten crisis in the region. There is a huge humanitarian crisis at the moment. Human rights actors and the media are not able to access Cabo Delgado [province], and that is a huge issue that we continue to focus on," Chagutah said.
The report says that there has been little reform in Zimbabwe since the exit of the late former President Robert Mugabe. Activists as well as supporters and leaders of the opposition continue to undergo harassment, arbitrary arrests, detention, torture and imprisonment without trial, according to the report.
Vongai Chikwanda, Amnesty International deputy director for southern Africa, spoke at the briefing about the detention of Citizens Coalition for Change member of parliament and Vice Chairperson Job Sikhala as one of many examples of state abuse. Sikhala has been in prison since June.
"The fact that Job Sikhala has not been convicted of any crime is worrying. What we have seen is a pattern of clampdowns on journalists, any opposing force or anyone who expresses any form of dissent. This just doesn’t go to opposition members, it's even within the general public, and this is concerning," Chikwanda said.
Shenilla Mohamed, executive director of Amnesty International, said South Africa is on the wrong side of human rights.
"Violent crime continues to plague South Africa and the right to life and security of person enshrined in the constitution as well as the universal declaration of human rights is violated daily with murder rates soaring as well as mass shootings, femicide and assassinations continuing unabated," Mohamed said.
Eswatini has also been cited for a growing government crackdown on activists, the abduction of opponents and recent murder of human rights lawyer Thulani Maseko.
Gender-based violence and the infringement of the rights of the LGBTQ community are also dark spots in some countries, including Zambia, the report said.
With countries like Zimbabwe, which has experienced election violence, set to go to the polls this year, Amnesty International is calling on governments to stop silencing peaceful dissent and allow journalists and human rights defenders to do their work.
South Africa, Zimbabwe and other countries in the region have not yet responded to the findings.
However, during a recent state of the nation address, South African President Cyril Ramaphosa vowed to redouble the government’s efforts to fight crime, gender-based violence and the delivery of basic services to citizens.
Zimbabwean President Emmerson Mnangagwa has previously denounced allegations of human rights abuses as "divisive falsehoods."
The government spokesperson for Eswatini, Alpheous Nxumalo, has also denied the involvement of authorities in human rights violations, including the shooting of human rights lawyer Thulani Maseko.
