The British Society for Immunology says the low rate puts infants and those with weak immune systems at particular risk, and has called for government action to boost uptake.
Babies normally receive the so-called six-in-one jab, which protects against six serious infections including polio, whooping cough and diphtheria, in the first few months of their lives.
But new Public Health England data shows that only 94.7% of those in North Yorkshire who had their first birthday in the six months to March had the vaccination.
It means 138 children in the area missed out on the injection.
North Yorkshire falls just short of the 95% vaccination rate recommended by the World Health Organisation to prevent outbreaks.
Across England, the vaccination rate for the jab was 92%.
Professor Arne Akbar, president of the British Society for Immunology, described the low rate as “concerning”.
He said: “Lower vaccination rates mean that these diseases can potentially spread within our communities, with unvaccinated babies and individuals with compromised immune systems particularly at risk.”
Professor Akbar said the Government should work with the NHS and councils to ensure vaccination services are accessible and that reliable information is available.
He added: “Vaccination saves lives and is one of the safest and most effective methods we have to prevent disease.
“We owe it to our children to make sure we do all we can to provide them with that protection.”
Babies should have three rounds of the six-in-one vaccination at eight, 12 and 16 weeks of age.
It helps them develop a strong immunity to diphtheria, hepatitis B, haemophilus influenza type b, polio, tetanus and whopping cough.
The NHS describes all of these as “serious childhood diseases”.
Jessica Morris, a research analyst at health think tank the Nuffield Trust, said the percentage of babies receiving the jab by their first birthday had fallen for six consecutive years in England.
Dr Mary Ramsay, head of immunisation at PHE, said: “Vaccination is essential to protect children from killer diseases.
“When it comes to vaccines, evidence suggests that parents trust the advice of healthcare professionals but the timing and availability of appointments can sometimes make it difficult for busy families to get their children vaccinated.
“We have a fantastic NHS vaccination programme but more can be done to achieve the best possible protection for everyone.
“Sending out reminders and making GP appointments as convenient as possible will make the biggest difference.”