Inkawasi: an early Inca administrative-military center (alternatively spelling
Incahuasi). In ruins, it is near the city of San Vincente de Cañete.
Willkawaman: another important administrative center and a large city during Inca era (alternatively sepelling
Willka Waman). Modern city of Vilcashuáman.
Wilkapampa: capital of the neo-Inca. Hispanicized as Vilcabamba, but currently known as Espiritu Pampa. Alternatively, this title could also be
Antawaylla, the Quechua name of modern Andahuaylas.
Qusqu: capital of the Inca.
Raqch'i: famous for being a control point for the Inca road system and for its temple. Alternatively spelled as Racchi. In ruins nowadays.
Hatunqulla: (or Hatun Colla/Hatun Qulla)capital of the Aymara kingdom of Colla (or Qulla). Located between modern cities of Puno and Juliaca, near Titicaca.
Naska: more the name of the region and its peoples than a particular city. The most important Nazca (culture) city was
Cahuachi (close to modern city of Nazca), but this city was apparently abandoned long before the Inca conquest.
Mawk'allaqta: a large urban, probably religious, complex in the region. In ruins nowadays and located in San Antonio, a small city in Arequipa department.
Ari Qepay/Ariqipa: another case of a name more of the region than a city. There was several small towns in the area during Inca era and many of them that still exist, but I gave preference to a name that ensures a nice historical continuity.
Mukiwa: (alternative spelling Muquehua, modern Moquegua) was an old city that existed since Tiwanaku era. Alternatively, it could be
Takana, which was the name of a region that gave the modern Tacna its name.
Chuqyapo Marka: this is the historical and current name of La Paz in Aymara language, originally refered more to the region than the particular settlement. The city itself existed since pre-Inca era, although was small back then.
Samaypata: an Inca city/fortress located in the border between their empire and Guaranis peoples. Modern Samaipata.
Pariya: apparently was the main Inca administrative center in Bolivian Altiplano. Although I know that we cannot found cities in salt flats, I've added just as an alternative city name. Nowadays is the small town named Paria.
Chuqichaka: another case of a name more of the region than of a particular village and is the modern Quechua name of Sucre. The city itself was founded over a indigenous Charca town with same name. Alternatively, it could also be
Huruncuta (or Oruncota), an Inca provincial capital between modern Sucre and Potosí currently in ruins, or even
Q'ochapampa (or Kochaj-pampa), a city that became the modern Cochabamba.