A memo signed by Gordon England, the second-highest official at the defence department, stated that all detainees are entitled to humane treatment.
Certain prisoners held during the so-called war on terror have not previously been given the protections of the Geneva Conventions - international agreements governing the treatment of prisoners of war.
The memo was made public on Tuesday as congress began hearings on how to proceed with the trials of Guantanamo prisoners. The supreme court ruled two weeks ago that the military tribunals set up by the Bush administration to try foreign terrorism suspects were illegal.
The US has faced international criticism over how detainees at Guantanamo Bay in Cuba and Abu Ghraib prison in Iraq have been treated.
The memo, dated July 7, stated that detainees held in US military custody across the world are covered by Common Article 3 of the Geneva Conventions of 1949.
The article prohibits violence against detainees, including mutilation, cruel treatment and torture, and "outrages upon personal dignity" including humiliating and degrading treatment". It also ensures care for the sick and wounded.
The administration said the admission was not a change in policy because the defence department already treated detainees humanely.
"It is not really a reversal of policy," said Tony Snow, the White House spokesman. "Humane treatment has always been the standard, and that is something that they followed at Guantanamo."