President Omar Hassan el-Bashir formed the committee after more than 100 people died in the clashes, the worst seen in decades in Khartoum.
The rebel movement's pullout from the committee was in protest at a police raid Tuesday in a camp outside the capital housing thousands of southern Sudanese.
The SPLM position is a break from the initial unified position it displayed with the Khartoum-based government to quell the unrest that polarised the capital's nothern and southern communties.
Under a peace deal in January, the SPLM returne to Khartoum and its new leader was sworn in as first vice president last week.
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