Mr O’Brien was due to leave at the end of next month, and Government sources have confirmed that Mr O’Brien, who earned €185,000 a year as director general, will not face any financial penalty or sanction.
He announced his departure on Thursday amid a maelstrom of controversy over when he knew of the cervical cancer test scandal.
The HSE and the Department of Health would not reveal the full details of Mr O’Brien’s exiting terms.
But a spokeswoman for the HSE said he would be entitled to a pension in line with public service norms.
Public service pensions begun before 2013 are worth up to one and a half times the person’s final salary by way of a tax-free lump sum plus an annual pension of half of their final salary.
A Department spokeswoman told the Irish Examiner that Mr O’Brien’s full contractual arrangements will apply.
On his last day, Mr O’Brien took to social media and criticised how TDs questioned him at the Public Accounts Committee (PAC) on Thursday.
Without referring to anyone by name, Mr O’Brien tweeted about how people conduct themselves at committee meetings.
When I appear in public - say at a Committee I conduct myself against a simple standard. Would I be happy for my children or my mother to see how I behave? I sometimes look across the room and hope their children will never see and hear how they behave.— Tony O’Brien (@tweetstob) May 11, 2018
Sinn Féin TD David Cullinane, a member of the committee, rejected the criticism by Mr O’Brien.
He said PAC members “ask the hard questions without fear or favour” and will continue to do so.
The party’s health spokeswoman Louise O’Reilly said she did not believe it was a mature thing for Mr O’Brien to have tweeted.
Fianna Fáil TD Marc MacSharry said: “The taxpayer pays my wages. They also pay Mr O’Brien’s. They have a right to criticise, question us, and scrutinise the decisions we make. Mr O’Brien does not seem to get that this is about the women involved and not him.”