But Guantanamo officials say the new facility is necessary to carry out their mission of holding men deemed to be "enemy combatants" by the US.
Robert Durand, a US navy commander, said 42 detainees have been taken to the new 178-cell prison in Cuba.
About 100 men who have been cleared for release and are awaiting transfer to another country are among more than 400 currently being held at Guantanamo.
The concrete-and-steel prison was originally designed as a medium-security facility.
"Asymmetric warfare"
Guantanamo officials say the new design aims to isolate prisoners and reduce their ability to communicate with each other.
Detainees confined in individual cells will now look out through long, narrow windows on areas with metal tables and stools that were originally intended to be shared living spaces, but which will now be off-limits.
An open-air recreation area has been divided into smaller spaces, which will hold only one detainee at a time.
Shower doors have been redesigned so prisoners' hands and feet can be shackled by guards before they leave the stalls.
"Anti-jump" fencing has also been installed along catwalks.
Durand said: "The new, climate-controlled camp is designed to improve life for both detainees and the guard force."
He said the new facility will allow the US naval base to close Camp 3, which was built in 2002.
Kris Winter, a US navy commander, said the modifications will help to protect guards after a clash between detainees and guards in May and also the suicides of three inmates on June 10.
Harry Harris, the commander of the prison, described the suicides in Camp 1 as "an act of asymmetric warfare against us ... not an act of desperation".
Camps 5 and 6 are reserved for the prisoners who are considered to be least compliant - an assessment the US military says it bases on whether detainees follow the rules of the camp, rather than on how they co-operate with interrogators.