The national average for take-up of the human papillomavirus (HPV) vaccine for 12 and 13 year-olds is 86%, but in Cornwall it is 57%.
Cancer charities called for the vaccine to be introduced in local schools.
Some GPs claimed the figures do not reflect the true picture. NHS England said the data was being reviewed.
It also said it was reviewing the delivery system in the South West but that the county's rural nature made a schools-based programme "more challenging".
The vaccine is offered in schools across most of England, but in Cornwall 12 to 13 year olds must see GPs for the jabs.
Robert Music, chief executive of Jo's Cervical Cancer Trust, said the vaccine would "have a major impact on reducing incidences of cervical cancer" in the UK.
"We have been calling for a couple of years now to change how the programme works in Cornwall," he said.
"A schools-based programme means you can offer it to kids while they're at school rather than having to take them out to have the vaccine twice."
The HPV vaccination is offered in two separate injections over a one-year period but up until last year it was three jabs. It protects against two strains of the sexually transmitted infection believed to cause 70% of cervical cancer cases.
Uptake in Cornwall has remained well below the national average for the past five years.
However, Dr Sarah Gray, GP Specialist in Women's Health, said the way the figures were recorded was misleading: "What NHS England have counted is the number of jabs in a school year.
"If they don't quite get all three within a year it looks like we've failed," she said.
She also said Cornwall was doing well at immunising older teenage girls.
Louise Blenkinsop from Falmouth, 32, recovered from cervical cancer in 2013 after "gruelling treatment" and was left unable to have children.
"It is ridiculous that Cornwall is being overlooked. Provision should be made equal across the country," she said.
NHS England is responsible for commissioning the vaccine on behalf of Public Health England.
A spokesman said: "Cornwall is a very rural county with a number of factors which make a school based model logistically more challenging to deliver than it would be in many other parts of the country."
He said the system was being reviewed "to assess both clinical effectiveness and value for money" and that checks were  being done on last year's data to make sure it was accurate.

Sunderland forward Duncan Watmore was on the fishing boat in Barbados when it was hit, and broken in two, by a catamaran.
He managed to haul three elderly passengers out of the water from the boat just before it sank.
His father, Ian Watmore, said the catamaran had "just ploughed straight into the boat and ripped it in half".
"They saw it and just assumed it was going to go round them and, when they realised it was coming straight at them, they started yelling and screaming but nothing changed," he said.
"These catamarans are quite powerful and the blade just ripped the thing in half."
Watmore had been in Barbados in February, recovering from an operation on a cruciate knee ligament injury, when the crash happened.
One of the guests on the boat had just had a hip replacement, one could not swim and the other was over 80, his father said.
After the crash, his son "clambered up on to the catamaran" and lifted them, and the skipper, out of the water just as their fishing boat sank, he said.
The 23-year-old footballer used his T-shirt as a tourniquet for the woman's leg, which was "bleeding heavily".
It was only afterwards that "shock started to set in", Mr Watmore Snr said.
"All the guests were coming up to him and telling him what a hero he was and I think the whole thing was just very disorientating for him," he said.
The rescue had been a good test of the strength of his knee, though "not one you'd plan", he added.
It is not known how the catamaran came to hit the fishing boat but it is believed its skipper was taken away by police.
Girls in Cornwall who are not being vaccinated against cervical cancer are missing a "life-saving opportunity", a charity has said.
[NEXT_CONCEPT]
A Premier League footballer saved three holidaymakers after a boat crash, it has emerged.