https://www.google.com/maps/place/13%C2%B042'20.0%22S+75%C2%...
It seems obvious to me they were made by the landing pylons of heavy-lift alien spacecraft.
At 1m diameter and 75cm deep, so ~0.59m^3, I calculate that to fill the Albert Hall, which a search suggests "has been estimated at" ~100,000m^3 (feels low to me, but it's quoted in many places), it takes around 170,000 of these Peruvian holes.
https://imgur.com/gallery/lni-enigma-of-amigara-fault-junji-...