The 15-member council unanimously passed a resolution allowing light arms to be sold to the Somali armed forces as they seek to rebuild and spread government authority into territory taken from the Al-Qaeda-linked Shabaab.
The embargo was imposed in 1992, a year after the fall of dictator Mohamed Siad Barre as rival warlords battled for control of the East African nation.
A transitional government, backed by an African force, is just starting to establish itself after major victories against Shabaab.
With US support, President Hassan Sheikh Mohamud, who took office in September, has been pressing for an end to the embargo.
Britain, France and other countries on the council had been more reluctant to fully lift the blockade because of the risk of heightening insecurity in a country already awash with arms, diplomats said.
Resolution 2093 allows for a one year suspension of the embargo when small arms will be allowed. The Security Council pointedly listed surface-to-air missiles, guns, howitzers and cannons, night vision equipment and related ammunition and components as items that cannot be sold to Somalia.
The 12.7mm limit on weapons means the Somali government will not be able to purchase anything bigger than a large calibre machine gun.
The government will have to give at least five days notice of deliveries to the UN’s Somalia sanctions committee and purchases will be monitored by UN experts. The government will have to report twice a year to the UN on weapons purchases.
Britain’s UN ambassador Mark Lyall Grant, whose country drafted the resolution, acknowledged that some countries thought it was “premature” to lift the embargo. Council members Guatemala and Argentina expressed strong reserves at the meeting.
But Lyall Grant said “The council has struck the right balance. It sends a positive signal to President Hassan Sheikh but it continues to give the council oversight of weapons flows into Somalia.”
“If over the coming year it is clear that this suspension of the arms embargo is being abused then we will take action accordingly in the Security Council,” the British envoy said.
US ambassador Susan Rice called the easing of the embargo “a clear signal of support” to the Somali president. “We will continue to work to support the government of Somalia as they endeavour to turn the page on two decades of civil war,” Rice said in a statement.
The resolution also gave a new one year mandate to February 28, 2014 to the 17,000 strong African Union force in Somalia, AMISOM. Though the troops are African – from Burundi, Djibouti, Kenya, Nigeria, Sierra Leone and Uganda – the European Union and United Nations pays most of the cost.
As government control increases, the UN Security Council is expected to move toward making the force a formal UN peacekeeping mission.
The resolution said the government must use the African force’s recent successes against Shabaab to build “sustainable, legitimate and representative local governance and security structures” in Mogadishu and other areas recovered from the Islamists.
The United Nations is to set up an expanded political mission in Mogadishu to help the government and coordinate efforts to counter the Somalia’s major humanitarian problems.