There are hundreds of prisons throughout Eritrea. In addition to the known prisons in police centers that are administered by Prison Department and those in army camps, there are a large number of secret prisons. Nekhra's prisons in Dahalak Island, Mai Sroa prison in Asmara suburbs and Ed Omer prison in Baraka-El Gash region are the worst and cruelest prisons in the country. In all the Eritrean prisons, there are vaults for political detainees for whom the authorities do not allow visits. Also, these vaults are used to punish other prisoners who disobey the authorities. There are open-space-prisons like prisons in army camps in Adi Abito near to Asmara, in Barnto and other places. There are prisons where containers are used as cells in Assab and Sawa camp, west of the country. More than 50 persons are put in one container and the prisoners must sleep in rotation. The detainees are not allowed to shower in prisons except once per week. In open-space-prisons, the prisoners take their bath in stagnant pools and whoever misses his turn for any reason he must wait until the next week. Prisoners are not allowed to use the bathroom except once per day which makes some prisoners use cans for urinating. Not showering and urinating inside cells cause the spread of lice among the detainees. In most prisons, there are no physicians and patients must be transferred to far-away places for medication. Because of malnutrition (a prisoner is given a loaf of bread and cup of tea two times per day), many prisoners arrive hospitals in a deteriorated condition and most patients who come from these prisons die.

Prisoners in Nekhra prison, the exiled and those accused of not performing the national service, are forced to work for the Eritrean Naval Forces without wearing shoes in high temperatures. Some prisoners who were expelled from Malta were afflicted with paralysis and relatives had to carry them when they were released. Most of the detainees got skin diseases and alopecia. Some Army generals force prisoners to work in their own farms or building their houses without payment. A former prisoner, Tsfai Tsfadhin, in a statement to Swuera Center said that during his detention he worked in a farm owned by a general in the army called Wody Gelta. Tsfai spent most of his prison duration in a cell underground in a place close to Barnto city.

The prisoners are exposed to various types of torture including standing under the sun until they went unconscious, beating with sticks, binding hands and legs in a figure-eight shape, binding in a way called "helicopter", and binding with trees.

Lesan Eldin El Khatib is a Sudanese national who had been detained from 4/12/2002 to 14/10/2004 without any accusation presented against him. He spent his detention in Wengl Marmara prison in Asmara. In his first days of detention, he was put in a cell underground and he did not know the day and the night until a small lamp was turned on. In his first day he heard voice of a woman screaming as she was beaten in the next door cell. He had been hearing that screaming for all the days he spent in the cell.

Punishment of beating and other types of torture is extensively used in the Eritrean prisons, especially to extract confessions of the prisoners. In a statement to Swuera Center, a Sudanese detainee, journalist Amir Babkir Abd Allah, said he was detained in Asmara on 1/4/2004 and transferred to the Headquarters of Eritrean Borders Forces in Asmara. He spent 24 hours in their office, his hands were bound to a chair and then he was transferred to Truck B prison in Asmara. He was put in a truck with another 150 Eritrean detainees and then they were transferred to the west of the country on 2/4/2004. Some prisoners were sent to prisons of Hicota, Sawa and Kiro. The truck arrived to the last destination the following day to a prison called Adr Sar close to Germaiaka administered by the Eritrean Intelligence. In this prison there are 50 detainees. Adr Sar prison was built underground and only the administrative offices can be seen. There are three rooms in the prison, the largest one is 12*4 meters square and the other two are 9*4 meters square. In addition, there are 12 cells for women; the largest one is 2*2 meter square. Amir said that he was one of 90 detainees who shared a cell of 9*4 meter square. The detainees were forced to work in prison, breaking stones from hills that surround the prison in the hottest times of the day and they were fed with dry bread and hot water.

There are reports about rape cases especially in Wengl Marmara prison in Asmara where officers summon the detained women to assault them sexually at night. This prison is supposed to be only for interrogation.