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Islamic Relief, one of few international aid agencies able to work in al Shabaab-run areas, said it had not been notified by the rebels that its permit had been revoked and that a ban would also threaten access to areas under government control.
Faced with a military offensive by African Union and Somali forces, the al Qaeda-linked insurgents have pulled out of a number of urban strongholds in southern and central Somalia. They still hold sway over vast rural areas where the central government and regional administrations have minimal control.
Al Shabaab accused the humanitarian organisation of working with other relief groups it had already expelled.
"Islamic relief was found to be covertly extending the operations of banned organisations, particularly WFP," al Shabaab said on Twitter, referring to the United Nations