Haji Sadeeq, a spokesman for the health workers, said the circumstances, especially in Jamrud area of Khyber Agency, were not favourable for his colleagues to take part in the three-day campaign.
"We feel threatened and everyone is frightened after the killing of our colleagues last month," he was quoted as saying by the Dawn daily.
He said it was not possible for health workers to conduct the door-to-door campaign because of the presence of militants in Jamrud.
Anti-polio campaigns in the tribal belt have been hit since the Taliban banned vaccinations in June 2012, saying the restriction would last till the US stops drone strikes.
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Militants and gunmen frequently attack vaccination teams, accusing them of being Western spies and part of a plot to "sterilise" Muslims. Dozens have died in these attacks.
A member of the local paramedics association said none of the "front-line workers" had been consulted when their office-bearers announced the end of an earlier boycott on Wednesday.
Health officials had earlier said they expected to vaccinate 50,000 children below the age of five against polio in Jamrud.
Pakistan is one of only three countries where the crippling disease remains endemic.