One in three state secondary schools in Wales say they don't have enough chemistry specialist teachers and more than half report a shortage of physics specialists.
The "worrying" shortage is revealed in a UK-wide science teacher survey by the Royal Society of Chemistry.
There is heavy criticism in the report of the use of non specialist teachers who are described as being just "one lesson ahead of students" in science subjects they don't have degrees in.
And one in five of the specialist science teachers that are in schools plan to leave within the next five years - citing workload and pay rather than planned retirement.
The society said there is no data on how many teachers have a degree in the specific science subject they teach, even at A level - so "specialists" are considered those with a degree in the science they are teaching, or with another science degree but long experience of teaching that subject.
