Much of the architecture of the site is in a poor state of preservation, having been subjected to looting and amateur excavations attempting to locate valuables since shortly after Tiwanaku's fall. This destruction continued during the Spanish conquest and colonial period, and during 19th century and the early 20th century, and has included quarrying stone for building and railroad construction and target practice by military personnel.
Another issue for archaeologists is the lack of standing buildings at the modern site. Only public, non-domestic foundations remain, with poorly reconstructed walls. The ashlar blocks used in many of these structures were mass-produced in similar styles so that they could possibly be used for multiple purposes. Throughout the period of the site certain buildings changed purposes causing a mix of artifacts that are found today.
Detailed study of Tiwanaku began on a small scale in the mid-nineteenth century. In the 1860s, Ephraim George Squier visited the ruins and later published maps and sketches completed during his visit. German geologist Alphons Stübel spent nine days in Tiwanaku in 1876, creating a map of the site based on careful measurements. He also made sketches and created paper impressions of carvings and other architectural features. A book containing major photographic documentation was published in 1892 by engineer B. von Grumbkow. With commentary by archaeologist Max Uhle, this was the first in-depth scientific account of the ruins.
In the 1960s, an attempt was made at restoring the site, but by very uninformed parties. The walls pictured to the right, of the Kalasasaya, are almost all reconstruction. The original stones making up the Kalasasaya would have resembled a more "Stonehenge" like style, spaced evenly apart and standing straight up. Unfortunately, the parties that made the reconstructions decided to make the Kalasasaya be enclosed by a wall that they themselves built. Ironically enough, the reconstruction itself is actually much poorer quality stoneworking than the people of Tiwanaku were capable of.[citation needed] It should also be noted that the Gateway of the Sun, that now stands in the Kalasasaya, is not in its original location, having been moved sometime earlier from its original location.
Modern, academically sound archaeological excavations were performed from 1978 through the 1990s by University of Chicago anthropologist Alan Kolata and his Bolivian counterpart, Oswaldo Rivera. Among their contributions are the rediscovery of the suka kollus, accurate dating of the civilization's growth and influence, and evidence for a drought-based collapse of the Tiwanaku civilization.
Archaeologists like Paul Goldstein argue that the Tiwanaku empire ranged outside of the altiplano area and into the Moquegua Valley in Peru. Excavations at Omo settlements show signs of similar architecture characteristic of Tiwanaku such as a temple and terraced mound. Evidence of similar types of cranial deformation in burials between the Omo site and the main site of Tiwanaku is also being used for this argument.
Today Tiwanaku is a UNESCO world heritage site, and is administered by the Bolivian government.
Recently, the Department of Archaeology of Bolivia (DINAR, directed by Javier Escalante) has been conducting excavations on the Akapana pyramid. The Proyecto Arqueologico Pumapunku-Akapana (PAPA, or Pumapunku-Akapana Archaeological Project) run by the University of Pennsylvania, has been excavating in the area surrounding the pyramid for the past few years, and also conducting Ground Penetrating Radar surveys of the area.
In former years, an archaeological field school offered through Harvard's Summer School Program, conducted in the residential area outside the monumental core, has provoked controversy amongst local archaeologists. The program was directed by Dr. Gary Urton, Harvard, expert in quipu, and Dr. Alexei Vranich of the University of Pennsylvania. The controversy had to do with the fact that permission to excavate Tiwanaku, being such an important site, is only provided to certified professional archaeologists and rarely to independent Bolivian scholars who scarcely can present proof of funding to carry on archaeological research. On that occasion permission was given to Harvard's Summer School to allow a team mostly composed of untrained students to dig the site. The controversy, charged with nationalistic and political undertones that characterized the archaeology of Tiwanaku  faded rapidly without any response from the directors. However, the project did not continue in subsequent years.

Restoration work
In 2009 state-sponsored restoration work on the Akapana pyramid was halted due to a complaint from UNESCO. The restoration had consisted in plastering the pyramid with adobe, despite it being unclear whether the result would bring the pyramid back to its original state.

Lukurmata
Lukurmata was an important secondary site near Lake Titicaca in Bolivia. First established nearly two thousand years ago, it grew to be a major ceremonial center in the Tiwanaku state, a polity that dominated the south-central Andes from 400 to 1200. After the Tiwanaku state collapsed, Lukurmata rapidly declined, becoming once again a small village. The site also shows evidence of extensive occupation that antedates the Tiwanakan civilization.

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