The report confirms allegations made recently by the United Nations High Commissioner for Refugees (UNHCR), and is likely to place the new government under renewed pressure to share power with other political groups.
The new government's human rights record and the question of what to do with those responsible for the genocidal massacres that took place in April are crucial to the country's future stability.
They will also have a big impact on the future of 2 million Rwandans, mostly Hutus, living in refugee camps in the region. Many of those who fled believe that the government of the Rwandese Patriotic Front (RPF) and its military wing, the Rwandese Patriotic Army (RPA), will kill them if they return.
The RPF has always portrayed itself as the clean- handed protector of human rights. However, today's report will badly tarnish that image and make it difficult for the international community to provide unconditional financial aid to the new government in Kigali.
Amnesty says that while the massacres by militias loyal to the defeated Hutu extremist government were well reported, human rights violations by the RPF have escaped widespread press attention. Movements of foreigners, including journalists, in areas ruled by the RPF, have been closely monitored.
However, during a recent visit to Rwanda and to Rwandan exiles in neighbouring countries, an Amnesty delegation found 'substantial evidence of severe ill treatment and attempted execution by the RPA, in addition to numerous testimonies about killings and other abuses which were so consistent in dates, places and names as to not be dismissed as anti-RPF propaganda.
'Many of the killings took place in a series of arbitrary reprisals mainly against groups of Hutu civilians . . . There were also sporadic deliberate and arbitrary killings as the RPA took control and, uncovering genocide, took indiscriminate revenge on unarmed Hutu civilians,' the report says.
Similar allegations were made recently by the UNHCR, but they were denied by the UN force in Rwanda, Unamir, whose spokesman said that if killings were taking place, UN troops would know about them. The disagreement led to a serious rift between the two UN bodies.
Amnesty says it showed the evidence of killings to the Kigali government in September, but has not received an adequate response. It recommends the government to set up a commission of inquiry, and to submit its findings to an impartial and competant court of law.
'The international community must not make excuses for or turn a blind eye to human rights violations committed by the RPA . . . on the grounds that they are not 'as serious' as those committed by its predecessor,' the report says.
However, Amnesty argues that the killings by the RPF cannot be compared to the genocidal massacres that took place when Hutu extremists murdered their political opponents and minority Tutsis between April and July this year.