The Somali government denies responsibility for alleged human rights violations, but will allow a visit by Louise Arbour, the UN High Commissioner for Human Rights.
"Clearly, there were major problems, major abuses during that period," Holmes said.
Ethiopian forces helped Somali troops rout the Union of Islamic Courts movement from south and central Somalia, including Mogadishu, at the start of the year.
Fighters opposed to the government have since then mounted an armed campaign against soldiers and Ethiopian troops, with violence peaking during March and April in Mogadishu.
Two bouts of heavy clashes in March and April resulted in more than 300,000 people fleeing Mogadishu, and triggered what the UN called "the world's worst humanitarian crisis".
Holmes said aid was reaching only 35 to 40 per cent of those in need due to difficulties linked to access and security.
"In terms of numbers and access to them, Somalia is a worse displacement crisis than Darfur or Chad or anywhere else this year," he said.
Aid workers complained that Somali authorities had failed to clear food shipments for distribution and said they were being harassed at checkpoints.
Since then, the government has promised to clear obstacles in providing aid to tens of thousands of people.
The EU is to also step up humanitarian assistance, and is ready to help disarm, and re-integrate fighters opposed to the government.