Unidentified gunmen abducted the six from an airstrip near the town of Dusamareb.
"The Secretary-General most strongly condemns the abduction of four aid workers and two pilots," said a statement issued by the UN headquarters in New York.
An aid worker in Dusamareb, who requested anonymity, said the four were employees of a French NGO, Action Against Hunger, and were running a nutritional programme for children.
"Three vehicles with about 20 armed men came on to the airstrip and took them," said the aid worker.
The aid worker said the team was driven toward the town of Eil Buur, about 100km southeast of Dusamareb.
Mahamud Nur Antoobo, an elder in Dusamareb, told IRIN residents were "extremely angry" and wanted the aid workers released. He said the abductors should release the six immediately.
"These people were our guests and they were here to help us," he said. "Attacking them is like attacking us."
Antoobo said elders were meeting to discuss how best to ensure the aid workers' release. "We will do anything and everything to get them back."
Attacks on the rise
On 29 October, two UN staff members working in Hargeisa, the capital of the self-declared republic of Somaliland, were killed following a suicide bombing at the UN Development Programme (UNDP) compound.
In early October, two Somali staff members working for UN aid agencies - one for the World Food Programme (WFP) and the other for the UN Children's Fund (UNICEF) - were shot dead in separate incidents.
In his statement, UN Secretary-General Ban Ki moon said he was "deeply concerned about the worsening trend of killings and abductions of aid workers in Somalia", and called upon all parties "to respect the neutral and impartial status of humanitarian staff, and to allow them to do their work bringing vital life-saving assistance to millions of Somalis".
The spate of killings and kidnappings is forcing many aid workers and civil society activists to lie low, said the aid worker.
"There is so much fear that no one wants to take a chance. We are wondering when it will be our time. You cannot help anyone when you are worrying about your own safety," he added.
The worsening state of security, particularly in the capital Mogadishu and south-central Somalia, has hindered the work of local and international aid agencies trying to assist tens of thousands of people affected by the conflict.
The UN estimates that 2.6 million Somalis need assistance. That number is expected to reach 3.5 million by the end of the year.
Since fighting between Ethiopian-backed Somali forces and insurgents began in early 2007, about one million Somalis have fled their homes. Some 8,000 civilians have been killed.