Schools are being forced to raise funds to build sports halls and only half of all secondary schools have a gym, according to secondary school principals.
They say they are concerned that not all schools will be able to offer Physical Education as a Leaving Certificate subject as a result.
Yesterday, Minister for Education Richard Bruton announced the introduction of PE as a new examinable Leaving Cert subject, to begin initially in a small number of schools from next September.
However, the National Association for Principals and Deputy Principals says a survey found that among secondary schools that did have gymnasiums, only a quarter had been fully funded by the State.
The survey, commissioned by the Joint Managerial Body and carried out two years ago, also found that almost half had been built relying entirely on private funds raised by the school.
The NAPD says many schools do not have the gymnasium facilities or equipment required to implement PE as an examinable Leaving Cert subject.
It says it is vital that schools are given the necessary supports to ensure that PE can be offered to students in all schools.
The Department has asked schools to apply to take part in the pilot phase. A spokesperson for the Department of Education has told RTÉ News that schools must have good sporting facilities in order to be considered.
The NAPD says some schools are paying up to €7,000 a year from already stretched resources to hire gym facilities for students.
NAPD director Clive Byrne said while they welcomed the introduction of the subject, the country needed to ensure that the subject does not become available only to the best funded schools.
He said funding needed to be made available so that the subject could be rolled out to all schools.
The NAPD has also said it is concerned that the shortage of teachers at second level may affect the implementation of the new subject.
The Department of Education, however, says it believes there are enough qualified PE teachers.
Around 2,300 PE teachers are registered with the Teaching Council and the department believes there may also be other qualified PE teachers who have registered under a different subject.