Even as the world body's top aid official called for help, eight people were killed in the capital Mogadishu and the town of Jowhar.
"There has been a response but we need to do more," Holmes told reporters moments after landing in southern Mogadishu's K50 airport for his second visit to the troubled Horn of Africa nation in a year.
"It is very hard for aid agencies to operate in Somalia because of the general security situation," he said.
Somalia is considered one of the world's worst developing humanitarian crises yet very few aid agencies and NGOs have been able to establish permanent and efficient operations there.
"There are checkpoints everywhere and aid agencies are stopped at these points and at times charged a lot of money. This is what I intend to discuss with the president and the prime minister," Holmes said.
He later met President Abdullahi Yusuf Ahmed and the country's newly-appointed prime minister, nur Hassan Hussein.
Fierce fighting between Ethiopia-backed Somali forces and Islamist rebels has displaced at least 600,000 people from the capital Mogadishu since February and hampered the delivery of relief aid.
The latest heavy battles last month drove out nearly 200,000 people from the war-wracked capital, according to the UN refugee agency.
"This is obviously a very serious humanitarian situation in Somalia," said Holmes, who arrived under tight security.
Much of the fighting since the start of the year -- when Somalia's transitional government reclaimed power from an Islamist militia thanks to Ethiopian military intervention -- has concentrated in Mogadishu.
But on Monday, a deadly clash erupted in Jowhar -- some 90 kilometres (55 miles) north of Mogadishu -- between members of the security forces over unpaid salaries.
According to residents and local officials, at least three were killed and more than 10 wounded in the fighting.
A security official speaking to AFP on condition of anonymity explained that the trouble started when disgruntled security forces robbed money collected by the police in protest at delays in the payment of their salaries.
At least five other civilians were killed by stray mortar shells and bullets in northern Mogadishu's Suqaholaha neighbourhood, residents said.
"I have seen four bodies near my house, three of them were killed by a mortar while the other was hit by a stray bullet," said resident Warsame Ali.
Abdihakim Subed told AFP his brother was killed as he headed to school in Suqaholaha, one of the most volatile zone in the seaside capital.
Holmes, in Somalia after a four-day visit to Sudan, was also expected to visit Afgooye -- west of Mogadishu -- where an estimated 200,000 people are living rough in squalid camps along the road.
During his first-ever visit to Somalia in May, Holmes was forced to cut short his two-day trip after an explosion hit a vehicle near the UN compound and killed four people.
Bloody clan bickering and power struggles that intensified after the 1991 ouster of dictator Mohamed Siad Barre have scuppered numerous initiatives aimed at stabilising Somalia.
SOURCE: AFP, December 3, 2007