Five health agencies out of 43 voluntary bodies have so far responded to a Health Service Executive request to confirm that they are operating in line with public pay policy.
Minister for Health James Reilly said ten more agencies have sought more time to respond.
Speaking in Belfast, Mr Reilly said Government policy is very clear and these agencies are covered by public pay policy and are expected to comply.
He was responding to a report that the Chief Executive of Our Lady's Children's Hospital Crumlin is receiving a €30,000 allowance from shops on campus.
The minister said it was open to each health institution to make a business case to the Department of Health for the arrangements put in place.
He said he had not received the confirmations required and if these are not received shortly, the department will have to take further action.
He said he was aware there were other arrangements which need to be corrected and brought into line with public pay policy.
Mr Reilly said additional non-pay monies that arise from other activities in the private sector, such as car parks and shops, cannot be used to supplement pay.
He said if there are specific pay arrangements and business cases that can be made, the department can look at that with Department of Public Expenditure and Reform.
Crumlin Hospital said its chief executive has a contractual entitlement to payment of an allowance for the supervision of auxiliary activities, income from franchises and change management.
This payment is non-pensionable and does not come from HSE or charitable funds.
It said the income stream used to pay the allowance is generated from profits from shops on the hospital campus.
The hospital said the allowance is a private contractual arrangement between the board and the chief executive.
The information was provided to the recent HSE audit on a confidential basis and is protected under data protection legislation.
On that basis, the hospital will not be making any public comment on the salary details of the private contract.
Service arrangements with health agencies under Section 38 of the 2004 Health Act state that providers shall "not pay nor subsidise salaries, expenses or other prerequisites which exceed those normally paid within the public sector".