Despite the recent signing of a peace deal, a group of rebels have set up a parallel administration in Virunga National Park.
UN peacekeepers say landmines have also been planted along one of the main routes through the region.
The area is home to more than half of the world's mountain gorillas.
"They have to go," said Diddy Mwanaki, a senior ranger for the Congolese Institute for the Conservation of Nature (ICCN).
"They are very aggressive against the rangers of ICCN, and have threatened to execute any of us who return to the gorilla sector."
He added that the group of rebels had also started taking tourist groups into the area to see the mountain gorillas.
"At the moment, we reckon they are taking about two groups per week, which generates money for their militias.
"Unfortunately, they are not - as far as we can tell - respecting the basic regulations to ensure that the gorillas are kept safe from disease and disturbance," he wrote on his blog, set up by conservation group WildlifeDirect.
The latest development in the stand-off between the rebels and wildlife groups in the area has come as a blow for conservationists working in the area.
Following the signing of a peace agreement to end the conflict between rebel groups and the government in January, rangers were hopeful of quickly returning to the Gorilla Sector of the Virunga National Park.
"The ICCN rangers had initially planned to spend seven days at Bukima before heading out to Jomba," explained Rob Muir, a Frankfurt Zoological Society researcher based in the area.
"However, the night before the operation was due to commerce, we received a call from Monuc (UN peacekeeping force) informing us that the road to Bukima had been mined.
"The only option therefore was to try and reach Jomba, right in the heart of rebel territory," he told BBC News.
At an earlier meeting, rebel leader Laurent Nkunda had said he was keen to see the rangers return to the area and resume monitoring of the gorillas.
But Dr Muir said the ICCN advance party had been stopped shortly after entering the area by rebels during an "aggressive and hostile" meeting.
"Director Norbert Mushenzi was informed that his ICCN delegation had only been let in out of respect for Monuc, and that it would be the first and last time they would be given access.
"They added that if it was not for the presence of Monuc, the delegation would have been executed."
He said conservationists were extremely worried about the formation of the rebel's parallel administration in the Gorilla Sector.
"The ICCN are concerned about the ultimate destination of the tourist receipts, as well as the capacity of dissident rangers under rebel control to properly manage the tourists in order to minimise the likelihood of human-to-animal disease transmission."
Facing the future
Virunga National Park, Africa's oldest national park, is home to an estimated 380 mountain gorillas, more than half of the apes' entire population.
As well as the risk of contracting human diseases, the animals are also under threat from poaching and habitat loss.
During 2007, 10 of the great apes were killed, including the execution-style shooting of five members of the Rugendo family in July.
Rangers believe illegal charcoal traders were behind the killings because the corpses were left where they fell and there is a huge demand for the fuel, which is the main energy source for local communities.
If left unchecked, conservation groups say only 10% of the animal's existing habitat will remain in 20 years time.
In an effort to increase protection of the gorillas, the governments of DR Congo, Rwanda and Uganda joined forces in February and launched a conservation plan to halt the destruction of the region's forests.
The 10-year project focuses on the tropical mountain forests that straddle the borders of the three nations.
Although ICCN rangers are unable to enter Virunga's Gorilla Sector, with the help of UN forces, they have had a number of recent successes in stopping illegal charcoal shipments leaving the area.
International conservation groups are currently discussing the possibility of organising a meeting between rebel commanders, the UN and conservation bodies, with the aim of reaching an agreement acceptable to all sides.