Unicef will begin the vaccination campaign in the self-declared autonomous northeastern region of Puntland on Friday.
The programme, intended to inoculate millions of Somali children against polio, will start in the breakaway state of Somaliland in the northwest on Saturday and in central Somalia on 24 June, it said.
"The outbreaks of polio in Ethiopia and Yemen, coupled with large population movements between Somalia and its neighbours, have put Somali children at risk of polio," Unicef said in a statement.
Outbreaks in neighbouring Ethiopia and Yemen have already paralysed 230 children and infected as many as 40,000 and threaten a resurgence of the disease in Somalia which has been polio free since 2002, it said.
"It is crucial that all efforts are made to ensure that the polio virus is not allowed to reverse the gains made so far in Somalia," Unicef said, noting that the anarchic country has no health infrastructure to deal with infections.
"Outbreaks of polio in Ethiopia and Yemen, coupled with large population movements...have put Somali children at risk"
The programme in Somalia is part of a broader UN effort to stem the spread of polio across Africa.
The resurgence of polio, blamed on a suspension of vaccinations in Nigeria for ideological reasons, has adversely affected a UN programme to eliminate the disease worldwide by the end of 2005.
Somalia, a nation of about 10 million people, has been torn apart by factional warfare since the overthrow in 1991 of strongman Mohammed Siad Barre.&n