Leila Zerrougui, head of the UN stabilization mission to the Democratic Republic of Congo, MONUSCO, said the provinces of Tanganyika and South Kivu and parts of North Kivu province were most at risk.
"I have grown increasingly alarmed over the situation in Beni in recent months, where we continue to face major challenges in implementing our mandate," she added.
"There is a potential for armed group interference in elections in specific areas throughout eastern DRC," she said.
Her remarks were made on Monday at the UN Security Council's monthly meeting on the DRC, Presstv reported.
The eastern DRC has been troubled for decades by inter-ethnic bloodshed and militia violence, a crisis that has escalated this year.
The city of Beni, home to up to 300,000 people, is under threat from the Allied Democratic Forces (ADF), a shadowy armed group rooted in Ugandan extremism that has killed hundreds of people since 2014.
The region is also battling an Ebola outbreak that has left more than 200 dead.
The unrest is running in parallel with a conflict in the central region of Kasai, casting a shadow over the country's ability to stage elections on December 23 to succeed President Joseph Kabila.
Zerrougui said many hurdles had to be overcome for the elections to proceed smoothly and be credible. The official start of campaigning is on November 22.
"It will be especially important for the government to take steps in the coming weeks to secure polls, particularly to ensure the participation of women, who make up 50 percent of registered voters," she said.
Zerrougui is also the UN secretary-general's special representative in the DRC.
MONUSCO, whose mission is now 17,000 strong and among the UN's largest, has been in the DRC since 1999. It has an annual budget of $1.153 billion (1.02 billion euros).