Only 49.8% of them are educated to chemistry degree standard - which is the worst figure in the UK.
In response, the Royal Society of Chemistry (RSC) launched a campaign on Wednesday to give students in Wales a world class science education.
The organisation is campaigning for the Welsh government to raise standards by 2020.
The RSC wants every chemistry pupil over 14 to be taught by a specialist teacher and all primary schools to have access to one.
"I was really lucky to have specialist chemistry teachers at my comprehensive school and tertiary college in Swansea," said the RSC's Jon Edwards.
"But many Welsh science students don't have that luck, their teachers need more support to be confident and knowledgeable about chemistry.
"Otherwise wise we risk falling even further behind both the rest of the UK and many countries around the world."
The Welsh government said it has introduced financial incentives to attract students to teaching science.
A spokesman said: "We want to support and encourage our best graduates to train to teach in Wales.
"That's why we've put in place new financial incentives of up to Â£20,000 for top postgraduate students who want to train to teach priority subjects such as maths, physics and chemistry in Wales.
"These incentives will continue to strengthen the quality of initial teacher training in Wales by encouraging the most talented graduates with high level subject specialism to enter teaching."
Fewer than half of chemistry teachers in Welsh secondary schools have degrees in the subject, it has been revealed.