Somalia's al Shabaab militants said they had banned Muslim aid agency Islamic Relief from areas under their control, depriving 1.3 million people of food, clean water and health care.

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aid agencies able to work in al Shabaab-run areas, said it had not been notified by the rebels that its permit had been revoked and that a ban would also threaten access to areas under Government control.

The al Qaeda-linked insurgents have pulled out of many urban strongholds in southern and central Somalia. They still hold sway over vast rural areas.

"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' food agency, World Food Programme (WFP).

Iftikhar Ahmed Shaheen, Islamic Relief's regional director, said: "We have no programme, as far as I am aware, funded by WFP."

The militants, who abandoned their last urban stronghold of Kismayu late last month after an assault by Kenyan and Somali troops, expelled the International Committee of the Red Cross (ICRC) from parts of the country under its control in January.

That followed the expulsion of WFP which has had no access to areas under al Shabaab's control since January 2010. Locals and relief organisations accuse al Shabaab of blocking emergency food aid during a famine in 2011 that ravaged southern Somalia.

WFP told Reuters it had not been working directly or indirectly with any other aid group in rebel-controlled territory in Somalia since then.