Machu Picchu was built by Pachacuti Inca as a royal estate and religious retreat in the mid 15th century. After his death, it remained the property of his allus (kinship groups), who were responsible for its maintenance, administration and continuing construction. As a remarkable sacred site, both in terms of location and execution, it surely was visited by Topa Inca and the last great ruler, Huayna Capac, although each in turn built his own estates and palaces in other locations. Few outside the Inca's retainers would have known of Machu Picchu’s existence, as travel was severely restricted except by Inca decree.  

Huayna Capac and an estimated 50 percent of the population died of smallpox around 1527. Inca governmental capability must have suffered greatly, resulting in a period of turmoil. The empire fell into civil war over Inca secession, and it’s likely that Machu Picchu was abandoned at this time because the cost of maintaining it was prohibitive, and the epidemic and war had depleted the remaining male population. 

Machu Picchu, primarily a ceremonial site, had limited administrative or commercial use and was located on a difficult road in near impassable terrain in the high cloud forest. It had little military value, located so high above an unnavigable section of the Urubamba River canyon. Most state- sanctioned traffic movement in Machu Picchu’s general direction to or from Cuzco and the Sacred Valley upriver would have been mainly via other Inca roads, either the high road near Salcantay or by the Lucumayo Valley road. 

It’s difficult to understand from our knowledge of Greek, Egyptian and other great early civilizations with written records how such a magnificent site could not have been discovered by the Spanish. Yet I can see how it happened: The Inca were a completely ordered and regimented society. Although great numbers of people were moved around for corporate state projects (mit'a) and resettlement, once at a location they did not move. The royal roads were reserved for official travel. Machu Picchu as a royal ceremonial estate was even more restricted, probably reserved solely to the Inca and other high persons. (Of course the city would have required a steady supply of outside goods. Also, like most Inca sites, it was undergoing continuing construction and must have had a resident crew of builders, attendants, farmers, etc.)  

The Incas were apparently able to control their remarkable state system through a pyramidal hierarchy, with information and direction flowing down through 10 overseers to 100, to a 1,000 and so on. We know from Spanish historians and the archaeological record that they did not possess an alphabet or written language, although they certainly must have utilized some symbols and diagrams. 

We know that the quipu (a collection of colored strings and knots) was extensively used as an accounting and record keeping device. This required a trained interpreter/programmer to accompany it. Although the quipu was known and used during the early colonial period, the technique for “reading” one was not documented and lost to history. The Inca also maintained a class or guild of oral historians who could recite detailed stories. What records the Inca state may have kept and how remain a mystery. 

With the catastrophic collapse of Inca social structure following arrival of the Spanish, these specialists/historians were scattered and forgotten. The Spanish, most of whom were illiterate, uneducated adventurers, had little interest in seeking or preserving anything not producing wealth and power. By the time scholars and responsible administrators arrived, the information was lost. 

When the conquering Pizarro arrived in Cuzco in 1532, Machu Picchu must have been mostly forgotten, and the few who remembered died without revealing its location to the Spanish. Machu Picchu or whatever its name at the time, would not have been of much importance to either the crumbling Inca state or the treasure-hungry Spanish. 

Manco Inca staged a country wide rebellion in 1536. After a failed siege of Cuzco, Manco, along with remnants of the court, army and followers, abandoned his headquarters at Ollantaytambo. Fleeing back into the remote Vilcabamba beyond Machu Picchu, he burned and destroyed Inca settlements and sites accessible to the Spanish. One of them was Patallacta, located at the start of the now famous trail to Machu Picchu from the Urubamba River. Of course, by this time the trail and the site itself would have been long overgrown and the approach blocked by seasonal landslides that so hinder backcountry travel in Peru. 

(Beyond personal observations and many trips to Machu Picchu, I have borrowed heavily from the excellent work of Michael Moseley, John Hemming, John Rowe and Johan Reinhard. Their writings are a must for anyone attempting an understanding of the Inca and the centuries of cultural development that preceded them.)