The UN Office for the Co-ordination of Humanitarian Affairs said on Tuesday that about 4,000 Somalis were stranded in the Somali town of Dhobley waiting to cross into Kenya.
The Kenyan government also blocked the Kenya Red Cross Society from entering the refugee reception centre in Liboi, about 550km northeast of the capital, where about 360 refugees were staying, UN officials said.
"We are certainly disturbed by reports we are getting that people seeking asylum are being sent back because this amounts to contravention of the international humanitarian law," said Millicent Mutuli, the spokeswoman for UN refugee agency (UNHCR).
The refugees had been fleeing fighting in Somalia, where government troops backed by Ethiopian forces are in the pursuit of vanquished Islamic courts fighters.
Kenya already hosts at least 160,000 refugees who fled fighting in more than 15 years of unrest in Somalia.