Moreover, 90 per cent have seen their workload increase and 31 per cent are covering for all or part of teachers' non-contact time, says the National Association of Head Teachers, which surveyed around 100 members across all 22 council areas in Wales.
It says heads are not getting enough workload reform cash to employ more staff, or are using the money to retain existing staff.
It also points to huge variations in payments to similar sized-schools, with primaries receiving anything from pound;6,300 to pound;51,000.
But the Assembly government says it has been "very clear" about funding the workload agreement, with another pound;70 million due in the financial year 2006-07.
Iwan Guy, NAHT Cymru's acting director, said around 34 per cent of members surveyed had opted to take on additional teaching staff to cover PPA, and 13 per cent had employed more support staff such as teaching assistants.
Heads and governors preferred qualified teachers to do such cover, he added, with one head noting: "We have experienced more class behavioural problems when support staff cover PPA time."
Mr Guy fears the increasing demands of the job will deter senior teachers from applying for headships - even though more candidates will be needed because of increasing numbers of retirements. A third of Welsh heads are aged over 55, according to figures from the General Teaching Council for Wales.
"The results of this survey will do nothing to attract deputies and assistant heads to apply for headship. Younger colleagues will be reluctant to step up to the mark when they see pressures on existing heads increasing. The worklife balance for many heads has worsened," he said.
The survey confirms findings from Estyn that workload reforms have added to the burdens on headteachers, and adversely affected their work-life balance.
But an Assembly government spokeswoman said: "Evidence from a range of sources, including the chief inspector's annual report, demonstrates that most schools are positive about the changes that the workforce agreement brings and have made excellent progress in implementing the necessary changes.
"We are already working with the Workforce Agreement Monitoring Group (WAMG) and other agencies to address work-life balance issues in schools."
WAMG is to publish a booklet on the elements of the agreement relating to heads, she noted.
Almost one in six headship vacancies in Wales was readvertised last year, compared to up to one in three in parts of England.