"We heard today that there was a very bad massacre in the area where we were in December," he said.
"And another massacre recently in February with perhaps another 100 people again."
Human Rights Watch said last month the LRA had killed 321 people in a previously unreported massacre in December.
DR Congo's government initially denied the massacre took place, but a local government official has since confirmed the killings but put the toll lower, at 188 people.
On Saturday, Holmes met a 23-year-old woman who was being treated by doctors after her lips and ears were ripped off in a trademark attack by rebels seeking to silence its victims.
Leontine Masini, another resident, spoke of a six-month ordeal that ended when she escaped as the fighters were asleep.
"They take wooden sticks and ask those who have been captured to hit someone with that stick on the head"
victim of LRA attack
"They take wooden sticks and ask those who have been captured to hit someone with that stick on the head. If you don't kill that person, you are being hit too," she said.
The 25 year-old said she had witnessed so many murders that "there is no way" to put a number on it.
"I did hit people. I didn't kill them, so I got hit, too," she saidd.
The violence comes as Joseph Kabila, the president of DR Congo, pushes for UN peacekeepers to begin withdrawing from the country bye the 50th anniversary of Congo's independence on June 30.
But Holmes warned that pulling out troops with the mission, known as Monuc, would damage the UN's ability to provide aid and help protect civilians.
"Our preference is for Monuc to stay and for any discussions of withdrawal to be based on not an arbitrary timetable, but on the accomplishment of what Monuc is there to do," he said.
"We are worried by the prospect of a rapid or premature withdrawal of Monuc because Monuc is very important for our activities in the sense of providing stability, providing security for humanitarians."
Campaign of attrition
A December 2008 US-backed military operation by the armies of Uganda, DRCongo and Sudan was meant to end the LRA's two decade-long rebellion, which had been based in DR Congo since 2005, when the group was forced out of northern Uganda.
But the group's leaders and many fighters escaped and the group has since splintered, carrying out massacres as it melted into the bush.
Holmes said there had been some "military successes", but said the scattering of LRA fighters had made them more dangerous.
"They have retained their capacity to commit those massacres," Holmes said.
International Crisis Group (ICG) think tank said of the hunt had "become a slow and very expensive campaign of attrition across three countries".
"It has also yielded unacceptably high human costs among local civilians, with virtually no accountability for the failure to protect," it said in a report issued last week.
"Only by pooling intelligence and coordinating activities across the entire affected region can the Ugandan army, its national partners, the UN and civilians hope to rid themselves of the LRA."