WWF ecologist Stephan Wulffraat told AFP that a live capture of the animal was required to confirm it was a new species.
The animal appeared to be a cross "between a cat and a fox" and may live in trees during the day, coming down at night, he said.
The group said it was extremely rare these days to discover a new mammal species of this size, particularly a carnivore.
If confirmed, it would be the first time in more than a century that a new carnivore has been discovered on the island, which lies between the Indian and Pacific Oceans.
The WWF warned that plans to create the world's largest palm oil plantation in Kalimantan, along the border with Malaysia's Sarawak and Sabah states, threaten further new discoveries.
The scheme, funded by the China Development Bank, is expected to cover an area of 1.8 million hectares (4.4 million acres).
Environmental watchdogs have criticized the plan, arguing that the jungle soil in the area is infertile and that the elevation is unsuitable for palm oil.
Indonesia is losing at least 2.8 million hectares of its forests every year to illegal logging alone.
The forest ministry's director for protected areas, Banjar Laban, told AFP that the potential discovery of a new mammal emphasized the urgent need to protect the biodiversity of Borneo's forests.
"If it turns out to be truly a new mammalian species, this should really become a national pride, something that the entire nation should be proud of and work to preserve," he said.
In the protected Kayan Mentarang forest, 361 new species — plants, insects, fish and other animals — were discovered between 1994 and 2004, he said.
Rapid deforestation has had devastating environmental consequences for both Indonesia and the Southeast Asian region, causing floods and landslides and shrouding nearby countries with haze from illegal fires set to clear land.