During an expedition to Papua's Foja Mountains in June, Conservation International (CI) and Indonesian scientists documented the two mammals - a Cercartetus pygmy possum, one of the world's smallest marsupials, and a Mallomys giant rat, the conservation group said in a statement.
Both mammals are currently under study and are apparently new to science, it said.
The scientists, accompanied by a film crew, also recorded the mating displays of several rare and little-known birds for the first time.
Scientists from the Indonesian Institute of Sciences and CI discovered dozens of new plants and animals on their first trip to the region, described as a "Lost World", in late 2005.
The giant rat is about five times the size of a typical city rat, says Kristofer Helgen, a scientist with the Smithsonian Institution in Washington DC, US.
"With no fear of humans, it apparently came into the camp several times during the trip," he says.
The Foja wilderness is part of the Mamberamo Basin, the largest unroaded tropical forest in the Asia Pacific region.
"It's comforting to know that there is a place on Earth so isolated that it remains the absolute realm of wild nature," says Bruce Beehler, vice president of Conservation International, who led the expedition.
With 42 million hectares (104 million acres) of tropical forests and some of the richest bio-diversity in the world, Papua is considered the one of the country's last rainforest frontiers. But it is under threat from increased clearing for palm oil plantations as well as illegal logging.