various stories covering the investigation:
Ahead of Bush visit, Colombia announces investigation into massacre
International Herald Tribune
by Toby Muse, 2/28/06

Just days ahead of a visit by President Bush, Colombia said it was investigating 69 soldiers accused in a massacre two years ago that induced Washington to suspend $70 million in military aid to the South American nation. read more, including a quote from FOR's John Lindsay-Poland

69 members of the Colombian Army declared suspects in February 2005 SJA massacre
Translated from the well-known Colombian weekly news magazine, Semana. original in Spanish

February 22nd: One of the most serious accusations in the history of Colombia’s Army, the military [brigade] is declared suspect in the dismembering of eight people, amongst them various children. Included in those declared suspects by the Fiscalía, [roughly the equivalent of the US Attorney General’s office,] are two military officers, 9 lower-ranking officers and 58 professional soldiers.

The Fiscalía clarified that there are not 56 soldiers, as was initially reported, but 69 soldiers that are declared suspects in the crimes of “homicide against a protected person” and “terrorism” for the massacre in San José de Apartadó. It was officially announced that the investigation, led by a prosecutor in the Human Rights Division, charged that two officers, nine lower-ranking officers and 58 professional soldiers have been charged with these crimes.

The Fiscalía also clarified that, with respect to the Peace Community of San José de Apartadó, the Inter-American Court on Human Rights had ordered provisional measures that imply, amongst other things, that the Colombian state provide special protection to the residents of this area.

This judicial action, comes two years after the massacre, ... one of the most horrifying events in [the department of] Antioquia and [will have] major international impact, as it concerns an action against leaders of a community with wide recognition. With this decision, doubts are being cleared up regarding the authors of these murders, in which five adults and three children, ages one, six and 11 were killed with a machete.

It can be said that many residents of the region where the massacre occurred, as well as Colombians in general, are breathing easier knowing that justice may be served. Without a doubt, however, it is troubling that the responsible parties may be 69 representatives of the State, amongst them a Captain in the National Army, whose mission it is to combat illegal [armed] groups and defend the civilian population, not to dismember two campesino families and hide their remains in communal graves.

The prosecutor of this case, who took two years to analyze the evidence and find the military responsible, has found sufficient evidence to merit to investigate them, and depending on their testimony, to resolve their situation in the courts. To start with, [the Fiscal] is saying that the version of events Army gave at the time of the massacre, in which they accused the FARC, is false.

Soldiers are declared suspects in the crimes of homicide against a protected person and terrorism, along with the February 21st, 2005 murders of Luis Eduardo Guerra, a representative of the peace community; his partner, Deyanyra Areiza Guzmán; 10-year-old Deiner Andrés Guerra; Alfonso Tuberquia Graciano; Sandra Muñoz Pozo, y her children one-year-old Santiago, six-year-old Natalia.

Initially, the investigation focused on the FARC as a result of information given by the Army. In the course of the investigation, however, it was established that some of the soldiers were lying in order to cover up to the truth.
...

A sad reaction
After reading the contents of a letter (cited in initial story, from Colombian NGO Justicia y Paz), President Alvaro Uribe appeared on television and rather than condemning the massacre, he focused on his assertion that the Peace Community was infiltrated by the guerrillas. Now, with the measure taken by the Fiscalía, it appears that the reality is, in fact, quite different.