I am aware of at least one instance - Ecuadorian rafts with masts and sails.
Spanish Accounts
There are many 16th-Spanish chroniclers who described these rafts, but here are three as an example:
1.Augustín de Zarate, page 15 in the link.
Estos balsas son hechos de unos palos largos y livianos atados sobre otros dos palos, y siempre los de encima son nones, comunmente cinco, y algunas veces siete o nueve . . . Hay balsas en que caben cinquenta homres y tres caballos, navegan con la vela y con remos, porque los indios son grandes marineros . . .
My translation:
This rafts are made of some long, light logs that are tied one on top of the other, and the ones on top are always an odd numbers, usually 5 but sometimes 7 or 9 . . . There are rafts that can hold 50 men and 3 horses, they use both sails and oars, because the Indians are great mariners . . .
2.Francisco de Xérez, p. 5 in the link.
Este navío que digo que tomo, tenya parecer de cavida de asta treynta toneles . . . Traye sus masteles y antenas de muy fina madera, y velas de algodon del mismo talle de manera que los nuestros navíos . . .
My translation:
This ship that I say I took must have had a capacity of nearly 30 toneles . . . it had masts and spars of very fine wood, and cotton sales of the same form as those of our own ships . . .
3.Miguel de Estete, p. 4 in my link
estas balsas son de unos maderos muy gruesos y largos; son tan fofos y livianos sobre el agua, como es un corcho . . . y de esta manera, poniendo un mástil en el madero mayor de en medio, ponen una vela y navegan por todas aquellas costas; y son navíos muy seguros porque no se puede anegar ni trastornar . . .
My translation:
These rafts are made of long, thick logs; they are as soft and light on the water as a corch . . . And in this way, putting a log mast in the middle, they add a sail and travel up and down all the coats. And their ships are very safe because they do not fill with water or overturn . . .
All three accounts describe these as large vessels with masts and sails.
Reconstructions
Some people have attempted to reconstruct these rafts based on Spanish accounts (including illustrations) and engineering principles.
In 1995 and 1998, John Haslett's team actually build two rafts and sailed them from Ecuador to Central America. The intention was to reconstruct possible routes used by sailors of the Manteño polity in Western Ecuador.
The most recent that I am aware of is Dewan and Hosler, 2008. They used mathematical and material simulations to conclude that these rafts could have made the journey from Ecuador to Western Mexico; they also postulated a possible timeframe.
Sources
Dewan, Leslie, and Dorothy Hosler. “Ancient Maritime Trade on Balsa Rafts: An Engineering Analysis.” Journal of Anthropological Research, vol. 64, no. 1, 2008, pp. 19–40. JSTOR, www.jstor.org/stable/20371179.
de Estete, Miguel. Noticia del Perú 1535.
Haslett, John F., and Cameron M. Smith. “In the Wake of Ancient Mariners.” Archaeology, vol. 55, no. 2, 2002, pp. 48–52. JSTOR, www.jstor.org/stable/41779658.
de Xérez, Francisco . Verdadera Relación de la Conquista del Perú 1534.
de Zarate, Augustín. Historia del descubrimiento y conquista del Perú 1572.