Around 5,000 children in the West Country are yet to be fully immunised against MMR.
Public Health England has released the figures as Prime Minister Boris Johnson visits the Royal Cornwall Hospital to announce plans to improve immunisation rates.
The agency is urging parents of children starting primary school in September to check their immunisation records.
According to PHE, some four and five-year-olds will be starting school next month at "unnecessary risk of serious diseases" because they aren't up-to-date with vaccinations.
In the UK dose 1 of the MMR vaccination protects against Measles, Mumps and Rubella and is usually given to children at around 12 months old.
The second dose is then given just before children start school to ensure the best protection.
Two doses of the MMR vaccine are needed for a person to be fully protected from the diseases.
Estimated number of children in the South West who haven't had their first dose of MMR. Source: PHE
Estimated number of children in the South West who may still need their second dose of the vaccine.
PHE said it's "particularly concerned about children being at greater risk of measles" due to outbreaks across the region in the past year.
It’s a real concern that so many young children in our region could be starting school without the full protection that the NHS childhood immunisation programme offers for free. We’re urging all parents of primary school starters to check their child’s Red Book now to make sure there is a record of two MMR doses and the 4-in-1 booster vaccine. If not, parents should contact their GP practice to arrange any further vaccinations that are needed. The vast majority of those affected are not fully immunised and vaccine preventable diseases spread more easily in schools. It’s crucial that children have maximum protection as they begin to mix with other children at the start of their school journey.
The warning from Public Health England comes as Boris Johnson is on his first visit to the West Country since becoming Prime Minister.
He's at the Royal Cornwall Hospital in Treliske announcing plans to improve immunisation rates after the UK has lost its measles-free status.
The new Prime Minister said "decisive action" was needed to improve rates and counter vaccine scepticism.