Tribesmen in Bajaur tribal district bordering Afghanistan refused to allow the vaccinations to take place after hearing rumours that the drive was a "US plot" to sterilise Muslim children, residents said.
"We have suspended the vaccination drive in Charming area after our vaccination team was kidnapped and beaten up by armed men there," local health director Chiragh Hussain Shah told AFP.
The health workers were held for four hours as their captors smashed vaccination kits, Shah said.
A Pakistani health official in charge of a polio inoculation campaign was killed in Bajaur in a bomb blast in February.
Health officials had been trying to dispel rumours -- sometimes spread by radio stations or from the loudspeakers of mosques -- that the polio campaign was a Western conspiracy to reduce Muslim populations.
World Health Organisation officials have said they still face difficulties gaining access to what they regard as "high-risk" tribal areas, including North Waziristan, Bajaur and Khyber.
Pakistan, one of only four countries where polio is still endemic, launched a nationwide vaccination drive Tuesday aiming to inoculate 32 million children against the disease.
The incidence of polio in Pakistan has been declining in recent years, with 11 new cases detected this year, compared with 40 in 2006.