"We could not immunise about 120,000 children due to insecurity and attacks on health workers," Abdullah Fahim, spokesman of the MoPH, told IRIN in Kabul.
Several polio cases have been reported in the southern provinces since 2008, and at least 22 cases of polio have been confirmed in the south, central and east of Afghanistan over the past 10 months, according to the MoPH.
More than seven million children under five were immunised against poliovirus and over six million given supplementary vitamin A capsules during a three-day nationwide immunisation campaign which started on 18 October.
The massive polio and vitamin A drive was conducted by 52,357 health workers in all 34 provinces of the country and was supported by the UN Children's Fund and the World Health Organization (WHO).
MoPH had raised hopes that a successful implementation of the immunisation exercise would rid the nation of the crippling disease.
The poliovirus has been eradicated all over the world except in Afghanistan, Pakistan, India and Nigeria, according to the WHO.
The inability of vaccinators to access and immunise children in insecure areas could spread the poliovirus among under-five children, health officials warned.
"We will not eradicate polio if we continue to miss children," said Mohammad Qasim, a health official in Helmand Province.
Taliban insurgents had previously given assurances they would not disrupt the immunisation campaign and would ensure safe passage for health workers in areas under their influence.
But gunmen believed to be associated with the insurgents reportedly attacked and then pillaged an immunisation campaign convoy in Uruzgan Province in October.
Health care providers were also threatened in Helmand and Kandahar provinces.
No Taliban spokesperson was immediately available to comment on the alleged attacks and threats to health workers.
The relatively calm northern parts of the country have been considered polio-free: the virus has not been reported there in the past three years.