The Sudan Liberation Army (SLA) and the Justice and Equality Movement (JEM) said 17 people were killed in Korbia in northern Darfur on Saturday and 13 died in attacks on Jabel Marra in the west on Sunday.
SLA spokesman Abdulrahman Musa said fighting continued in Jabel Marra on Monday, adding that the rebel groups had lodged a complaint with the African Union (AU), the mediator in the talks.
The AU has 3000 troops in Darfur.
"In the final analysis, we believe these [ceasefire] violations would not create a conducive environment to reach a settlement during this round of talks," Musa said at a joint news conference with the JEM.
A spokesman for the Sudanese government delegation at the talks said the two towns allegedly attacked were under AU control and it was up to the AU to confirm or deny violence.
"If they're talking about bandits then we don't control bandits," he added.
Rebel groups and Khartoum are
engaged in peace talks in Nigeria
The AU said preliminary investigations found no proof of fresh fighting in Darfur, a vast desert region in western Sudan.
"We have asked the SLA to give us the coordinates of the position where these attacks have taken place... As soon as they do that, we shall send our team to investigate and establish whether indeed such attacks took place or not," AU chief mediator Baba Gana Kingibe said.
Kingibe said the rebels had considered boycotting the talks but were persuaded to await the outcome of the AU investigation.
The SLA said last week that government forces had killed 10 fighters and at least as many civilians in attacks aimed at derailing the talks, which resumed last Thursday.
The JEM has accused AU troops of not doing enough to protect Darfur's people from government forces and their militia allies who the rebel movement says are still carrying out atrocities in the region.
"In the final analysis, we believe these [ceasefire] violations would not create a conducive environment to reach a settlement during this round of talks"
Abdulrahman Musa, spokesman, Sudan Liberation Army
The SLA and JEM launched a rebellion in early 2003 over what they see as discrimination and neglect by Khartoum, which responded by backing militias to drive non-Arab tribes from their villages, according to the rebels.
The conflict has caused tens of thousands of deaths and driven about two million people from their homes into overcrowded refugee camps in Darfur and neighbouring Chad.