First period of archaeological research (1993-2004)
Although COPESCO has made some critized restorations of the Archeological Complex, on the other hand it has done a great task in the recovery, restoration, recognition and sectorization of Choquequirao. Among the most suggestive discoveries was a pavement buried beneath the floor of the Ushnu. It is a rectangular geometric shape, divided into smaller rectangular or quadrangular spaces. It is oriented according to the four cardinal points, which agrees with the astronomical and calendrical functions that the ushnu had in Inca times.
It is important to know that one of the archaeologists of COPESCO, Percy Paz Flores, in an interview given to the writer Hugh Thomson (The White Rock), revealed some significant discoveries: a) at the time of abandonment, the inhabitants of Choquequirao were building other agricultural platforms , besides reconverting for agricultural use terraces that had once had ceremonial functions, and these works were left unfinished; b) several bodies (skeletons) have been found without burial, with obvious signs (broken skulls) of having been killed; c) many walls of the citadel had signs of being burned.
These data cast haunting shadows about the end of Choquequirao.
New archaeological research (2004-2005)
Following the intervention of the "Peru-France Fund", a scientific mission from France, led by archaeologist Patrice Lecoq, arrived in Choquequirao,
As demonstrated by the excavations made in 2004 by the french mission, the site of Choquequirao had several phases of pre-Inca occupation. According to the study of the domestic pottery found, a first period (between 1000 BC and 200 AD), a second one (between 500 dc and 1000 dc) and a third one (between 1000 dc and 1,400 dc); is also identified the Inca occupation, being "Inca local" and "Inca imperial" type ceramics.
Also architecturally, although some constructions belonging to the previous periods of occupation (in the Sector of Pikiwasi), have been recognized, it emphasizes that llacta grew, taking its definitive form and elegance, only under the inca occupation.