It says torture is widespread in a network of detention centres.
Some of those imprisoned are journalists or critics of the government, Amnesty says. Others have practised an unregistered religion, or tried to flee the country or avoid conscription into the army.
In most cases, prisoners' families are not informed of their whereabouts, and often never hear from their relative again.
"The government has systematically used arbitrary arrest and detention without charge to crush all opposition, to silence all dissent, and to punish anyone who refuses to comply with the repressive restrictions it places on people's lives," said Claire Beston, Amnesty's Eritrea researcher.
"Twenty years on from the euphoric celebrations of independence, Eritrea is one of the most repressive, secretive and inaccessible countries in the world."
The facilities used as detention centres include underground cells or shipping containers, Amnesty says.
The group says some prisoners are left for days in what is known as the helicopter position - lying face down with their hands and feet bound together.
It says it has received many reports of deaths in detention resulting from torture, the bad conditions or suicide.