It is odd that Apocalypto included conquistadors as contact was very late in the story of the Maya:

Meanwhile, the two remaining Raiders chase Jaguar Paw towards the coast, where all three are astonished at the sight of Spanish conquistadors making their way to the shore. As the two Raiders are confounded by the Spanish ships and begin walking towards the coast, Jaguar Paw uses the distraction to flee and return to his village.

https://en.wikipedia.org/wiki/Apocalypto

Although much reduced, a significant Maya presence remained into the Postclassic period after the abandonment of the major Classic period cities; the population was particularly concentrated near permanent water sources.[78] Unlike during previous cycles of contraction in the Maya region, abandoned lands were not quickly resettled in the Postclassic.

https://en.wikipedia.org/wiki/Maya_civilization#Postclassic_...

There was a good indie film a while back, On The Ice, that I believe only had native peoples in it. It's a contemporary setting, though.

https://en.wikipedia.org/wiki/On_the_Ice

Nobody’s old enough to remember Windwalker? A major release in 81 and subtitled.

If you actually look at the link prpi provided, there are several examples. E.g., Atanarjuat: The Fast Runner (yes), Hiawatha, and Kings of the Sun; if you allow animated films, there's Pachamama and The Emperor's New Groove. More recent examples not in that list include the Canadian movies Maina (2013) and Edge of the Knife (2018).