It is unacceptable for churches that failed to protect children from sexual abuse to still have charity status nine months after the royal commission delivered its final report, a former assistant taxation commissioner has said.

Terry Hamilton wrote to the prime minister’s office, the Australian Taxation Office and the Australian Charities and Not-for-profits Commission (ACNC) expressing concern at the number of unchallenged breaches of taxation law by Australia’s religious institutions.

The high court of Australia states for church bodies to qualify as religious institutions the church body must: be instituted for promotion of a religious object; its activities must reflect that character; and its practices and conduct must not offend against the laws of Australia.

The royal commission into institutional responses to child sexual abuse found more than 4,000 children were sexually abused in 1,691 different religious institutions, including 2,489 children sexually abused in 964 religious institutions managed by the Catholic church.

“These institutions attract significant financial benefits particularly through tax exemptions and charity status,” Hamilton said.

“The associated crimes in these cases breach the taxation law obligations that must result in a forfeit of tax exemptions and the registration of tax-exempt charities. I notified the prime minister and the treasurer of these breaches, in particular those relating to the Catholic church.”

Hamilton also notified the ACNC, whose role is to determine if an organisation meets the requirements of being a registered charity and to monitor the ongoing compliance of charities with the ACNC governance standards. The ACNC responded that if Hamilton wanted to raise a concern he could fill out a separate form for each specific charity he had concerns about.

An ACNC spokeswoman told Guardian Australia that it had closely followed the outcomes the royal commission and agreed some of the findings raised issue of appropriate governance of organisations, including registered charities.

“The ACNC is unable to confirm or comment on any investigations due to the secrecy provisions within our legislation,” the spokeswoman said. “However, one of our current areas of focus is on ensuring charities have appropriate governance in place to safeguard vulnerable people, particularly children.”

The ACNC has a range of compliance powers available when it finds deliberate breaches of the ACNC act or governance standards have occurred, including revocation of charity status, formal warnings and suspension or removal of responsible persons such as board or committee members.

Leonie Sheedy is the head of the Care Leavers Australasia Network (Clan), which represents those abused in children’s homes and foster care, including those run by churches.

Clan has long been calling for churches and charities that failed to protect children to be taxed. Sheedy said “nothing” had been done to hold the churches and charities to account by revoking their tax-exempt status since the royal commission completed its work in December. She also criticised the ACNC, which in July published information aimed at helping representatives of organisations participating in the national redress scheme to register as charities.

The National Redress Scheme was established to provide support, including financial redress, to people who have experienced institutional child sexual abuse.

“We support Terry Hamilton’s call for those churches and charities to lose their tax exemption,” she said. “It is too easy to get charity tax exemption in this country, and it should be immediately removed from any organisations where it has been found crimes were committed against children.”