Somalis are seeking aid in Kenya and Ethiopia, as well as in camps inside Somalia Continue reading the main story Mr Bowden told the BBC that aid was being given through al-Shabab's drought committees, which run the camps.
Mr Bowden said this could be done as long as the aid was delivered according to humanitarian principles.
He described the situation as so severe that it was vital to scale up aid operations inside Somalia.
The UN's refugee agency estimates that nearly one-and-a-half million Somalis have been forced from their homes but remain in the country.
But until very recently helping them has been very difficult indeed.
Al-Shabab, which rules over large swathes of south and central Somalia, had imposed a ban on foreign aid agencies in its territories two years ago, accusing them of being anti-Muslim.
It lifted the ban 10 days ago as long as groups had "no hidden agenda".
'Humanitarian principles'
Mark Bowden said that aid was being delivered to camps run by committees under the supervision of al-Shabab, despite the movement's known allegiance to al-Qaeda.
But he made it clear that this could only proceed as long as humanitarian aid was delivered free of any political connotations.
"The Shabab have, as I understand it, through their drought committees been distributing assistance to vulnerable groups of the population, so they have taken an interest and expressed concern.
"It is of course important to also recognise that the work that we do in these areas will be conducted under humanitarian principles and based on need and without any political association attached to the assistance," said Mr Bowden.
On Wednesday the UN has made its first aid delivery to drought victims in areas of Somalia controlled by the militants, since they lifted an aid ban.
UN children's organisation Unicef said al-Shabab had given UN workers unhindered access and hoped this would encourage other agencies.
'Close to famine'
Unicef airlifted food and medicine to malnourished children to the central town of Baidoa, more than 200km (about 125 miles) north-west of the capital, Mogadishu.
Extended drought is causing a severe food crisis in the Horn of Africa, which includes Kenya, Ethiopia, Djibouti and Somalia. Weather conditions over the Pacific means the rains have failed for two seasons and are unlikely to return until September.
Food shortages are affecting up to 12 million people. The UN has not declared a famine but large areas of the region are now classified as in crisis or emergency, with malnutrition affecting up to 35-40% of children under five.
The humanitarian problem is made worse by ongoing conflicts, which means that until July militant groups had only allowed aid organisations limited access to large parts of southern Somalia and eastern Ethiopia.
Since the beginning of 2011, around 15,000 Somalis each month have fled into refugee camps in Kenya and Ethiopia looking for food and water. The refugee camp at Dadaab, in Kenya, has been overwhelmed by 370,000 people.
Farmers unable to meet their basic food costs are abandoning their herds. High cereal and fuel prices had already forced them to sell many animals before the drought and their smaller herds are now unprofitable or dying.
The refugee problem may have been preventable. However, violent conflict in the region has deterred international investment in long-term development programmes, which may have reduced the effects of the drought.
Development aid would focus on reducing deforestation, topsoil erosion and overgrazing and improving water conservation. New roads and infrastructure for markets would help farmers increase their profits.
The result of climate conditions, conflict and lack of investment is that 6.7 million people in Kenya and Ethiopia are currently existing on food rations, and relief agencies estimate 2.6 million in Somalia will need assistance a new emergency operation.
The Unicef representative for Somalia, Rozanne Chorlton, said al-Shabab had assured the agency it could operate without undue interference.
"They gave assurances that our access for humanitarian purposes would be unhindered and that we would be able to reach the people who need support most," Ms Chorlton told the BBC.
Unicef paid no fees to al-Shabab, and that the success of the mission meant it would be repeated in the near future, she added.
She warned the situation was close to famine.
On Sunday the first in a series of UN refugee agency emergency flights arrived in Nairobi with 100 tonnes of tents.
The cargo was immediately off-loaded for transport by road convoy early in the week to the sprawling Dadaab refugee camp complex near the Kenya-Somalia border.
The flight was the first of five scheduled for Nairobi on alternate days this week from the UNHCR regional stockpile in Dubai.
http://www.bbc.co.uk/news/world-africa-14178953
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