Health Minister James Reilly has summoned heads of hospitals and health agencies to account for unsanctioned payments for executives.
The chiefs of bodies found not to be compliant with salary caps for the public service will be asked to explain where and why monies are being paid.
The demand for explanations was made after the HSE rejected claims that it agreed or sanctioned top-up payments for the chief executive and other senior staff in the Central Remedial Clinic.
Agency and hospital heads will be called in for meetings from next week.
Dr Reilly said he has requested urgent action to ensure all agencies in the health system comply with pay rules with answers expected before Christmas.
"The HSE has a team of senior managers following up with individual agencies," the department said.
"The HSE will take whatever actions are necessary to deliver full compliance and ensure that any governance deficits identified are comprehensively rectified immediately."
Former chairman of the Central Remedial Clinic Des Peelo has claimed that two of the top people in the HSE were at a meeting in 2009 when privately funded top-up payments for nine people in the organisation were agreed.
He said the top-ups were fully on the record with the HSE.
The executive denied the charge.
Dr Reilly received a report on breaches of salary scales under section 38 of the 2004 Health Act in recent weeks.
The controversy was sparked when the watchdog, the Health Information and Quality Authority (Hiqa), revealed in a 2012 report that some breaches occurred at Tallaght Hospital.
The HSE report into the issue found that the issue is a long-standing one that has been continuing for many years.
Mr O'Brien told an Oireachtas committee last week there had been a "nod and wink" culture in the institutions regarding the breach of earnings.
He revealed only seven of 42 hospitals and health agencies complied with public sector pay rules.
A review has found that in 2011 more than 3.2 million euro was paid out in additional allowances from state funds to senior managers.
Some payments above standard public sector salaries have been found to be above board, such as work done in the private sector.
Thirteen hospitals and health agencies have been found collectively paying more than 900,000 euro to executives from funds sourced privately.