The Welsh government is more than halfway through a £4.6m five-year programme to immunise badgers in north Pembrokeshire.
Infection rates have fallen across Wales, but Christianne Glossop said it was too early to say whether it has had "additional benefit".
Dr Glossop was speaking ahead of a worldwide conference on TB control.
It will be held in Cardiff on Monday.
"The programme is for five years," she told BBC's Sunday Politics Wales.
"We've completed two years and we're now well into year three, and so the results are by no means available yet."
TB infection rates fell across Wales over the last 12 months, she said.
"The reduction in north Pembrokeshire is in line with the national reduction, so right now, we have no evidence that the vaccination programme in badgers is delivering an additional benefit - and we wouldn't expect to see any evidence at this stage either," she said.
In 2012 and 2013, 2,776 badgers were trapped and vaccinated in the Intensive Action Area (IAA), which also takes in parts of Ceredigion and Carmarthenshire, at a cost of more than £1.8m.
But Dr Glossop said that the wider TB eradication programme cost £28m last year alone, most of which was spent on testing cattle, biosecurity and compensating farmers.
"You've always got to have the balance here between all the different elements of the programme, making sure that you're tackling all sources of infection," she said.
The vaccination programme was announced by Labour ministers in 2012 when they abandoned the previous coalition government's intention to cull badgers in the IAA.
It is unclear whether vaccinating badgers in west Wales has cut TB in cattle, the chief vet has said.