An al Shabaab official, who asked not to be named, told the news agency Reuters they had exchanged fire with French commandos.
Helicopters attacked al Shabaab at 2.00 am this morning. Two civilians died in the cross fire.
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Dozens of flood alerts have been issued for swathes of the country as heavy downpours and severe gales are expected.
Four migrants who tried to cross the Channel in an inflatable dinghy have reportedly been rescued by French coastguards.
The victim, a man in his 40s, is being treated in hospital for "life-changing" injuries after the attack by two men who remain on the run.