A faction of the Sudan Liberation Army led by Abdel Wahed Mohammed al-Nur and the rebel Justice and Equality Movement both refused to sign the agreement, citing a need for more political positions in a proposed government, a voice in the disarmament proceedings, and better compensation for victims of the conflict.
Another faction of the SLA had signed the peace deal with the Sudanese government on May 5, but the rivalries between the groups raised questions on how useful a peace deal could be if only one of the three factions agree to it.
The current signatories have said that no changes could be made to the deal as brokered in early May.
Khalil Ibrahim, the JEM leader, cautioned world leaders at a press conference to "be patient, not to hurry up, not to force an unacceptable peace on people of Darfur."
The AU is now left with the decision of whether or not to pursue punitive measures against the groups while simultaneously pushing for a peaceful end to the prolonged civil war.
The AU Peace and Security Council will meet soon to discuss placing sanctions on the rebel groups' leaders.
AU personnel have been targeted in the recent upswing in violence in Darfur and placed the responsibility for these attacks on the groups declining to sign the deals.