Some theories, controversial, have suggested exactly such contact between Japan and South America, particularly regions now in Peru and Ecuador. A overview of the hypothesis can be found in

http://books.google.com/books?id=C8GLGNrxxQMC&pg=PA398&lpg=PA398

Note that the above extract concludes that it was not likely, based on the evidence.

Other discussions include the following extracts :

Sites in central and southern Japan (Kozanji, Kutobo, Ubayama) yield Jomon (meaning cord-marks) pottery artifacts which are basically a brownish grey cord-marked ware and are widely distributed also in the Pacific, extending as far as Peru.
http://www.affs.org/html/ryukyuan_landforms.html

The Valdivia site on the Ecuadorian coast (contemporaneous with the late preceramic in Peru) has early pottery by about 3100-3000 BC. Dug by Meggers, Evans, and Estrada (1965). The ceramics are sophisticated. There is also clear evidence of contact or interaction with people down the coast for the exchange of Spondylus shells, but the archaeologists interpreted the site as demonstrating even longer distance contact - with Japan. According to Meggers, the pottery looked very much like the early Jomon wares of Japanese Neolithic fishers, who must have traveled across the Pacific and landed in Ecuador and brought it to South America.
http://www.indiana.edu/~arch/saa/matrix/saa/saa_mod03.html
Source(s):
http://books.google.com/books?id=C8GLGNrxxQMC&pg=PA398&lpg=PA398
http://www.affs.org/html/ryukyuan_landforms.html
http://www.indiana.edu/~arch/saa/matrix/saa/saa_mod03.html

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