Deputy health minister Hilmi Yahaya denied that any pig material was used.
"We are telling the people it is not true," he told parliament, in response to a question about the growing boycott in the mostly rural state of Kedah.
Hilmi did not say how many children missed their vaccinations due to the unsubstantiated concerns.
Swine is considered unclean in Islam, and consuming any part of it is strictly forbidden.
The Health Ministry has intensified its public information and education campaign to promote immunisation among children, especially in remote areas, Hilmi said.