When history is written it is oftentimes the victor whose voice is heard the loudest. I empathize with the Peruvian people, and all indigenous peoples, whose historical records have been taken from them, whether it be gold or silver artifacts, broken pieces of pottery, their tombs opened and invaded, or the corpses of long dead people taken from their homeland.
Universities, archaeological societies, independent explorers. All sorts of institutions and people have laid claim to their "findings". But, that should't discount that these findings will then reach a greater proportion of people than just a small number who know very well of the magical places that lay hidden from so many eyes. Many of the wider swath of people have expertise and knowledge that can maintain those historical sites and the artifacts within. That being said, it's deplorable for any entity or person to lay claim to treasures that are of great importance to the people whose ancestors were the creators thereof.
For what it's worth, I read this in the wiki entry on Machu Picchu:
On 19 September 2007, the Courant reported that Peru and Yale had reached an agreement regarding the requested return of the artifacts. The agreement includes sponsorship of a joint traveling exhibition and construction of a new museum and research center in Cusco about which Yale will advise Peruvian officials. Yale acknowledges Peru's title to all the excavated objects from Machu Picchu, but Yale will share rights with Peru in the research collection, part of which will remain at Yale as an object of continuing study.
On 19 June 2008, National Geographic Society's vice-president Terry Garcia was quoted by the daily publication, La República. "We were part of this agreement. National Geographic was there, we know what was said, the objects were lent and should be returned."
On 21 November 2010, Yale University agreed in principle to the return of the controversial artifacts to their original home in Peru.
La Casa Concha (The Shell House) located close to Cusco's colonial center will be the permanent site where the Yale University artifacts will be exhibited. Owned by the National University of San Antonio Abad Del Cusco, La Casa Concha will also feature a study area for local and foreign students.