The documents will be reviewed by a panel which will decide which papers should be declassified under a constitutional requirement that state material be made public automatically unless their release compromises national security.
Colom himself lost his uncle, politician Manuel Colom Argueta, during the war in a 1979 army ambush.
Between 80 and 90 per cent of the murders committed during the war were carried out by the army and presidential guard, a UN-backed truth commission found.
Many of the victims were indigenous Maya Indians.
However at the time the commission, which compiled thousands of interviews with victims following the country's 1996 peace accords, named no army officials, partly because then the files were not open to the public at the time.
Lawyers for the army have also attempted to block tribunals from obtaining access to the archives.
Waiting for answers
"We have been waiting 24 years for the state to give us some answers ... all I want is to find my son's remains"
Emilia Garcia, mother of disappeared union leader
Human rights officials are also sifting through thousands of recently discovered National Police archives - a group accused of kidnapping and torturing opponents during the war.
Rights groups say the army files will help solve war crimes because the police collaborated with the army and information can be matched up from the archives.
Many Guatemalans hope with the forthcoming release of the archives they will finally obtain information about their loved ones.
Emilia Garcia hopes the army files will contain clues about her son Fernando Garcia, a union leader allegedly shot by police in 1984, who was taken to a military hospital and then disappeared.
"We have been waiting 24 years for the state to give us some answers," she told Reuters news agency.
"All I want is to find my son's remains, he is not a lost dog."