Gary Brace was responding to new figures in the GTCW's annual digest that show the number of heads registered in 2007 had fallen from 1,797 to 1,758 on the previous year.
But they also show that 48 more women had taken the National Professional Qualification for Headship over the past year.
He said: "I believe that over time the NPQH qualification, which became a requirement for headship in 2005, will eventually have the effect of increasing the number of female heads."
More than 75 per cent of secondary heads are currently male.
Mr Brace also called for headship to become a more attractive proposition and encouraged teachers to strive for the NPQH, following the further recorded decline in head numbers.
"This could be due to the general decrease in the number of head posts due to schools closing or amalgamating," he said.
The figures also show that 42 per cent of heads speak Welsh.