John Holmes told the Security Council on Monday that the UN believes almost 400,000 people fled Mogadishu in recent fighting and the vast majority have not returned.
The government says that only 40,000 were displaced and about half have returned to the capital.
Holmes visited Mogadishu earlier this month and met Abdullahi Yusuf, the president, but his planned two-day trip was cut short when two explosions went off - one of them near the UN compound that killed three people.
During his brief stay, Holmes said, clan elders and representatives of civil society and women's groups expressed concern about intimidation and several said they were convinced the UN and the world had abandoned Somalia and weren't interested in the fate of the Somali people.
He said: "I assured them that this was not true and that my presence in Mogadishu was a symbol of the UN's deep concern, political as well as humanitarian.
"We all have a responsibility to ensure that this is indeed the case, and not to turn our backs on Somalis in their latest hour of desperate need."
Holmes said the recent massive displacement "has further compounded one of the most difficult humanitarian situations in the world, in a country affected not only by long-running internal conflict but also chronic food insecurity, alternating droughts and floods and endemic disease".
Those who fled are afraid to return because of violence, warnings by the government not to go back to so-called public buildings where they were living, the loss of homes and difficulties in moving, he said.