Update 5.36pm: St John of God's have released another statement disputing a claim by Health Minister Simon Harris that the HSE's final report found that the order "had diverted money due to service users, to pay top-ups and bonuses to senior executives".
The Hospitaller Order of Saint John of God said that funds meant for services had not been diverted.
The Order's statement said: "In a statement today in response to the HSE Internal Audit on Compliance with Public Pay Policy, Health Minister Simon Harris said that the Order had diverted money due to service users, to pay top-ups and bonuses to senior executives.
"As a point of clarification, there is no reference to any diversion of funds in the findings of the HSE Audit. The Order confirms that no such diversion of funds took place and there is no question of funds provided for services having been diverted."
Update 2pm: St John of God's have released a statement to confirm their receipt of the final report from the HSE.
They have said that The Hospitaller Order of Saint John of God and Saint John of God Community Services "has at all times co-operated fully with the HSE in the course of the audit review process".
They have stated that the report is detailed and that it will take time for them to properly review and assess the findings.
"Hospitaller Order of Saint John of God accepts there are lessons to be learnt," the statement said.
In terms of payments they stated that: "The Order has directly subsidised Saint John of God Community Services the sum of €16 million over the past four years alone. In addition, a portion of the salaries paid to executives was funded by way of a management charge paid by the Order to Saint John of God Community Services and therefore did not result in an additional cost to the Exchequer."
They have said that they expect to receive written communication from the HSE to follow-up on the recommendations in the report.
The statement concluded by saying that instead of responding to leaks in the media, they will engage with the HSE.
Earlier: The Health Minister says St John of God’s must pay back millions paid to staff in top-ups.
The Irish Times reported this morning on a HSE recommendation that the order repay €12m in secret payments over 30 years.
Minister Simon Harris says the payment of top-ups is clearly forbidden and must be given back.
"They need to make sure all of that money is repaid in full to services.
"I don't quite frankly buy the argument that because it came from a private source, not a public source, that it's not a matter for the State.
"Of course it is. Public pay policy is set out very explicitly that money should never have been diverted to pay top-ups, bonuses, side-payments, whatever you wish to call them and there's an absolute moral if not legal responsibility on St John of God's to repay that money back into services," he said.