Taxpayer-funded humanitarian aid worth £480,000 was captured by al Qaida-linked militants as they rampaged through southern Somalia.
The supplies were in warehouses seized by al-Shabaab and they were later believed to have been set ablaze, rather than stolen the Department for International Development (DfID) said.
Details of the incidents appeared in DfID's annual accounts which stated that there was no prior warning of the attacks and its partner organisations in Somalia were unable to move the supplies.
The accounts said the £480,000 was written off "following the theft between November 2011 and February 2012, by al-Shabaab in southern Somalia, of DfID funded humanitarian materials and supplies from the offices and warehouses of partner organisations, to which DfID had provided funding to deliver projects and programmes".
It continued: "DfID's partners had no prior warning of the confiscations being carried out and therefore had no time to prevent the loss by relocating goods.
"DfID continues to work with its partner organisations to ensure that risks like this are identified and that the organisations take appropriate action. This can include putting effective controls in place, where possible, to mitigate and/or eliminate such risks which reduce the effectiveness of our aid.
"While the theft suffered represented a stores loss, the property was not stolen from DfID stores. DfID funding was provided to purchase goods but no benefit was received by the end recipient due to the theft."
A spokesman for the department said: "DfID works in some of the most dangerous places in the world, including Somalia, because tackling the root causes of poverty and instability there ensures a safer world and a safer UK.
"Working in conflict-affected and fragile states carries inherent risk. DfID does all it can to mitigate against this but, on occasion, losses will occur.
"We work with our partners to design programmes that protect our investment from misuse or theft."