Researchers said they found German coins minted during World War Two in the ruins in northern Argentina.
The researchers said that the buildings were probably never used by fugitive Nazis, because they found they could live freely in Argentine towns.
Nazis who fled to Argentina included Adolf Eichmann and Erich Priebke.
The researchers from the University of Buenos Aires said they decided to investigate the buildings because of a local legend claiming they had been used as a hide-out for Martin Bormann, a close aide to Adolf Hitler.
The overgrown ruins are located in Teyu Cuare park, near the town of San Ignacio in northern Misiones province.
Researcher Daniel Schavelzon told Argentina's Clarin newspaper that the architecture of the three buildings differed markedly from that of others in the region and that their purpose in the middle of a remote nature reserve was a mystery.
He said that a number of objects had been found that linked the buildings to wartime Germany, such as coins minted in the late 1930s and early 1940s and a fragment of Meissen porcelain made in Germany.
However, none of the objects has so far been found to have any direct links to any Nazi officers.
Mr Schavelzon told Clarin that his team thought previous theories, such as that the building had been built by Jesuit priests, were "too simplistic".
He also dismissed the local legend that Hitler's private secretary Martin Bormann had lived there.
Mr Schavelzon pointed to DNA tests carried out in 1998 on a skeleton found in Berlin that proved Bormann committed suicide in 1945 and did not flee to South America as had long been rumoured.
The researcher insisted, though, that the buildings in Teyu Cuare park were very unusual.
He said the walls, some of which were 3m (9ft) thick, were "on an incredible scale".
He also said that their location was "completely inaccessible".
"You'd never be able to find them if you didn't know their exact location," he said.
He said the theory the team was currently working on was that the buildings were constructed as a hide-out by the Nazis in case they lost World War Two.
But he said he did not think it was ever used, as the Nazis found they could live in relative comfort in Argentine cities rather than have to hide in a remote jungle fortress.
Hundreds of Nazis and fascists, some of them wanted war criminals, were allowed to enter Argentina by the president at the time, Juan Peron.
Adolf Eichmann, the SS officer who oversaw the logistics of the Holocaust, famously lived in a suburb of Buenos Aires for years before being captured by Israeli agents.
In 2000, then-president Fernando de la Rua apologised for Argentina's role in providing a refuge for Nazi war criminals after World War Two.
Archaeologists are trying to determine whether ruined buildings in a remote nature reserve in Argentina were built as a hide-out for German Nazi officers.