The Mission comes as Somali government led by moderate president Sharif Sh. Ahmed which controls a few areas in the capital requested to train 6,000 strong police forces.
Al-Qaeda inspired Al-shabaab group which is trying to toppling internationally-backed President Sharif Sheikh Ahmed runs most of southern Somalia and parts of Mogadishu.
EU foreign ministers said in a joint statement after meeting in Brussels that they should continue to help stabilise Somalia by supporting the security sector and development. "Also assistance to the population and capacity-building support", the statement said.
"In this context, the EU council agreed to set up a military mission to contribute to training of Somali security forces," BBC stated.
France had begun training about 500 Somali troops at its military base in Djibouti last year.
4,500 Ugandan and Burundian troops are deployed in Somalia for backing the Somali government.
Uganda was ready to deploy over 8,000 troops to the AMISOM mission in Somalia.
Somalia has not had an effective government since warlords overthrew longtime dictator Mohamed Siad Barre in 1991.
Source: Africa New