The JEM's spokesman at the talks, Ahmed Hussein Adam, said a government security agent posing as a journalist had approached JEM leader Khalil Ibrahim in a hostile manner.
"He is not a journalist, he is a security personnel. He tried to approach (Ibrahim) holding a strange device ... Mr Khalil's guards tried to stop him but he kept coming ... They ended up hitting each other," Adam said.
"We condemn the government of Sudan for using the name of journalism and undermining press freedom by using journalist badges for security personnel," he added.
The Sudanese embassy official did not know details of the incident, and a spokesman for the government negotiating team could not immediately be reached for comment.
In Khartoum, the state-run Sudanese Media Centre reported the incident, saying the union of Sudanese journalists had condemned the "attack".
AU spokesman Nouredine Mezni said he was not aware of any incident on Friday. He noted that delegates from all parties had continued consultations through the weekend.
The talks, which started on Friday, aim to end more than two years of conflict in Sudan's vast western region of Darfur. Tens of thousands have died there and violence has driven more than two million from their homes into refugee camps in Sudan and neighbouring Chad.
Four previous rounds of talks in the Nigerian capital ended in stalemate.
The new round of talks has got off to a slow start, with disagreements over the role of delegates from Chad and Eritrea holding up proceedings.
A brief plenary session took place on Sunday, and the AU said a further face-to-face meeting would go ahead later on Monday after separate consultations between the mediators and the parties.
(Additional reporting by Opheera McDoom in Khartoum)