Rwanda President Paul Kagame.
The London-based rights watchdog said it had gathered evidence of "unlawful detention, torture and other forms of ill-treatment and enforced disappearances, mostly of civilians, at the hands of Rwanda's military intelligence".
Amnesty, in a report titled Rwanda: Shrouded in Secrecy, called on Kigali to reveal the "fate or whereabouts of all those subjected to enforced disappearance" and to investigate allegations of torture.
It alleged security services arrested suspects and held them in secret without informing their families, and had subjected them to beatings, electric shocks and made them make forced confessions.
Rwanda's justice ministry condemned the report, saying there is "ample provision for judicial review" and that any alleged reports of torture were treated seriously.
"As far as the specific allegations contained in this report are concerned, it was explained to Amnesty in June that the courts had indeed determined that some illegal detentions had taken place," a statement said.
"These occurred as a result of over-exuberance on the part of individuals within the security services and were dealt with through the courts which immediately put in place corrective measures."
Foreign Minister Louise Mushikiwabo said on her Twitter account on Friday "Rwanda will act on all credible claims of torture but won't engage in a shouting match with another NGO seeking headlines at Rwanda's expense". – Sapa-AFP