Rehab has said it provided the HSE with the details of senior salaries of staff in Rehab Care.
It has also been confirmed that the HSE has never sought, or been refused, the salary details of Rehab Group CEO Angela Kerins.
The HSE has said it has a contract with Rehab Care and the National Learning Network.
It said that since 2013, it has sought through the Service Level Agreements, the pay for senior staff for these bodies.
The HSE said it had no contract with the Rehab Group.
In a statement issued today the HSE also said: "The HSE has service arrangements in place with two wholly owned subsidiaries of the Rehab Group, namely Rehab Care and the National Learning Network (NLN).
"For the first time, in 2013, the HSE as part of Service Arrangements required that each of the organisations with which the HSE has a contractual relationship, provides details, by way of a standard template, of salaries of senior managers higher than Grade VIII, including the CEO, of such organisations.
"The HSE has received information from many of the organisations, including Rehabcare and NLN and is currently involved in a process of validating the information for completeness.
"A report on this information will be made available to the JCHC & PAC when the validation exercise has been completed over the next number of weeks.
"The HSE has never sought the salary of any named individual."
Minister for Health James Reilly said this afternoon that senior staff at Rehab should disclose their salaries to the public.
Mr Reilly said that anyone earning over €250,000 of taxpayers' money needs to be open and transparent about their pay policy.
He said that if Rehab was not going to cooperate, then the Government's relationship with the charity would come into question.
Oireachtas Health Committee chairman Jerry Buttimer had called on the board of Rehab to publish details of the salary paid to its chief executive.
It came after Rehab Group Chairman Brian Kerr said the issue of Ms Kerins' salary would be discussed at a special board meeting on 17 February.
Meanwhile, the Health Service Executive told Prime Time it had written to Rehab and all other Section 39 organisations on 10 December telling them they will be required to disclose senior manager remuneration.
Rehab had claimed that it had received no formal request from any relevant authority to disclose the salary of its CEO.