Some members of the vaccination team of 10,500 due to take part in the three-day polio campaign started administering oral vaccinations in parts of the troubled south and east, a spokeswoman with the UN children's organisation UNICEF said.
The remainder would be called into action over the coming days.
Afghanistan is one of a handful of countries where polio is still present.
Nine new cases of the paralysing disease have been reported so far this year in the south and east -- areas where violence has prevented vaccination, UNICEF spokesman Roshan Khadivi told AFP. There were 31 new cases last year.
"Most of these cases are in areas which are insecure, where there are military operations, there are Taliban operations and a lot of anti-government elements," she said.
The campaign targets 1.3 million children and has enlisted the help of community leaders to enable vaccination teams to move into areas they had previously not been able to access, she said.
The vaccination push coincides with a build-up to the United Nations' International Day of Peace on Friday, which has encouraged schools, non-governmental groups and government ministries to hold events urging peace.
A kite-flying ceremony is due Thursday while the women's ministry has called a minute's silence to remember the tens of thousands of people killed in Afghanistan's decades of war that started in the 1970s.
In the coming days, new parks are due to be opened in Kabul, schools are to be painted white and documentaries shown on the theme of peace.
Posters and "blue flags for peace" are strung up around the city and the United Nations Mission in Afghanistan issued a statement Wednesday calling for a "total cessation of violence countrywide" on Friday.
The head of the NATO military forces fighting the Taliban and trying to push reconstruction in Afghanistan, General Dan McNeill, has also lent his support.
"No one wants world peace more than the soldiers, sailors, airmen, and marines serving their respective countries as part of the International Security Assistance Force," he said in a statement.
The Taliban launched their insurgency after being driven from government in late 2001 and the violence has grown more intense every year, with more and more suicide bombings as well as all-out battles between rebels and troops.
Around 5,000 people have been killed so far this year, according to an AFP count, with most of the dead rebel fighters.