The Government hailed the figures as “fantastic” and said it will save lives.
But the numbers drop by more than half among teenagers who have left school.
All girls under 18 are eligible for the vaccine which was brought in a year ago and protects against HPV (human papillomavirus) which causes 70% of cervical cancer cases.
Participants get three doses over a six-month period.
Today’s figures show that overall uptake of the vaccine among girls in second, fifth and sixth year of secondary school over the past year is 93.5% for the first dose, 92.4% for the second dose and 87.7% for the third dose.
A Scottish Government spokeswoman said today: “It is fantastic that over 90% of girls in school who have been offered the HPV vaccine have chosen to protect themselves against the virus with at least one dose of the vaccine.
“The figures are testament to the hard work of NHS boards, particularly front-line nursing staff, in delivering this programme.”
She added: “We will continue our efforts to ensure that Scottish girls benefit from this vaccine, which will save lives, and the second year of the schools based HPV programme is already under way.”
Although girls are routinely offered the vaccine at school, there is also a catch-up campaign so those who have left school can be given it.
Interim figures for the latter group indicate that uptake is 43.1% for the first dose and 35% for the second dose.
But the Government says these figures do not provide the “full picture” and expects rates to increase.
The spokeswoman added: “We have always known that it would be more challenging to reach girls who have already left school, but health boards have been working hard to ensure that uptake is as high as possible.”
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