They believe vaccination will make their children infertile.
Despite efforts to sensitise parents in every ward, some of them remained unconvinced.
Some villages also not reached as the access roads still flooded.
More than 2000 children in Tana River County missed the first phase of the polio vaccination exercise conducted in early July.
Speaking at the Hola Level Four hospital, health promotion officer, Mr Josephat Ndegwa, said parents in Madogo, in Tana North, and Kipini, in Tana Delta, resisted the vaccination citing religious beliefs.
"Some of the parents in Madogo, especially fathers, protested the idea of giving their children the polio vaccine, claiming it was against their religious beliefs," he said.
Mr Ndegwa added that the people believe that the vaccination would make their children infertile, hence it took a lot of time to convince them, before a few could accept to bring out their children for vaccination.
Despite efforts to sensitise parents in every ward, some of them remained unconvinced, Mr Ndegwa said. He added that some villages were not reached as the access roads were still flooded, reiterating that plans were underway to ensure they were reached at the onset of the second phase of polio vaccination.
"Some of these villages are still flooded and there are no direct access routes, but we will reach them this time round and meet our target," he said.
However, the officers managed to vaccinate 65,400 children in the first phase out of the 68,008 that were being targeted.