Nigerian military helicopters have rushed polio vaccines to dangerous parts of the country's north east, where Boko Haram operates and where two toddlers paralysed by the virus were recently discovered, health officials said.
The World Health Organisation said the wild virus has circulated undetected for years in the area where the Islamic extremists have prevented vaccinations.
Borno state health commissioner Ibrahim Miringa said recent attacks by the Islamic extremists prevented the emergency operation from getting health workers to two parts of Borno state where the children with polio were found.
Boko Haram has killed polio vaccinators in the past.
He said the two children, aged under two, were among refugees recently arrived from areas newly freed from Boko Haram.
The apparent outbreak is major setback after Nigeria was declared polio-free in October.
Massive challenges face Nigerian health workers supported by the WHO and the US Centres for Disease Control to urgently vaccinate millions of endangered children in an area where the UN suspended aid after a military-escorted humanitarian convoy was attacked last month.
"Not all the areas that have been liberated by the military could be accessed by our health officials because of recent attacks in Jere and Gwoza local government areas carried out by Boko Haram," Mr Miringa said.
Jere and Gwoza are the areas where the first two cases of polio were found in Nigeria in more than two years, the WHO announced on Thursday night.
Nigeria's removal from the WHO's list of polio-endemic countries had meant all of Africa was free from the crippling disease. Only two other countries remain on the list - Afghanistan and Pakistan.
Mr Miringa said health workers have been vaccinating refugees as they arrive in major camps, "but recent liberation of internally displaced persons from the hinterlands and their being camped in satellite camps have made the immunisation exercise difficult".
International organisations plan to support Nigerian health workers in using "a hit-and-run kind of strategy", said the WHO director for polio eradication, Michel Zaffran.
A massive vaccination drive is starting in Borno and within weeks will be carried to nearby Benin, Chad, Central African Republic, Chad and Cameroon, he added.