The rebels said on Wednesday that Sudan - as an AU member state - had had input into the pan-African body's monitoring of the shaky April ceasefire but they were left without a voice.
"Since Saturday, we have boycotted the activities of the ceasefire commission," said Abd al-Rahman Fadul, who represents the Justice and Equality Movement (JEM) on the commission.
JEM and the Sudanese Liberation Movement (SLM) are the two main rebels groups in Darfur. Both are represented on the ceasefire commission along with the Sudanese government and AU officials.
"We have reservations regarding decisions being made without consultation with all the parties," Fadul said.
Darfur's rebels launched a revolt in early 2003, complaining of official neglect and marginalisation. Before the ceasefire, the fighting had killed and estimated 70,000 people and driven nearly 2 million from their homes.
Representatives to the commission in Darfur investigate reported violations of the ceasefire while other representatives meet regularly in Chadian capital of N'Djamena.
Mirghani Ahmad, another JEM representative to the commission, said the rebels were unhappy after not being consulted about increases in AU troops and police from AU member states patrolling Darfur with their Sudanese counterparts.
Officials from the SLM were not immediately available for comment but have previously said they were also boycotting the commission.
The JEM officials said they had informed the AU of their decision in a joint letter sent to the body last week but had yet to receive a response.