Paul Kiely, the former Chief Executive of the Central Remedial Clinic (CRC), received a pension package of €700,000 which was paid out of public donations to the charity.
The new €700,000 figure is on top of a €3 million transfer of funds from the Friends and Supporters of CRC fund, the Public Accounts Committee (PAC) heard today.
Earlier today, the PAC heard testimony from the HSE that the revelations came to light after it appointed John Cregan to take over the running of the CRC.
Mr Cregan was appointed to the position after the board of the CRC resigned en masse last month.
In a hearing before the PAC in December, it was stated that Paul Kiely had received €200,000 in a lump sum and that he would receive €98,000 a year by way of pension.
But the committee heard this morning that in addition to that amount, Mr Kiely received another €273,000, which was not disclosed when Mr Kiely and other CRC managers were before them in December.
It also emerged that a further €268,000 was paid to pension administrators Mercer in order to ensure Mr Kiely's retirement package would be based as if he worked until November 2016, even though he resigned in July 2013.
The HSE said the deal was subject to a confidentiality agreement but that there had been no approval for the deal, and that if it is found that the payments are in breach, steps would be taken to recover the money.
On foot of the information revealed at the committee, Independent TD Shane Ross said the PAC was "deliberately misled" by former members of the CRC board.
Brian Conlan, who succeeded Mr Kiely as CEO, and was a board member at the time, said he knew nothing of the massive pension package deal. "I knew nothing of this, this is all new to me. I am alarmed at what I have heard here," he said.
Mr Conlan said he felt he had to resign from his post as CEO before Christmas, because of the top-up controversy that had engulfed the charity.
"I felt it was the appropriate thing to do," he said.
Mr Conlan resigned at the height of the top-ups scandal before Christmas and has said he had no role in deciding his salary, which breached HSE guidelines.
Appearing before the Public Accounts Committee today, he said the public perception of public donations being "siphoned off" to pay the salaries of CRC bosses was not accurate. "That was not my understanding of how funds were managed," he said.
Mr Conlan told the committee his refusal to attend the committee before Christmas was because he had "just returned from his honeymoon in the United States where I was for three weeks and where I first learnt of the questions being raised".
"As you can appreciate, I was highly stressed by all that had transpired, particularly the tone and volume of the media coverage and I had just tendered my resignation from the CRC. Because of this, I was told I had no access to my files in CRC," he said.
"My home was literally besieged for days by journalists forcing my wife and I to leave for several days in order to maintain some level of privacy. I didn't have the time or resources to prepare adequately for such an appearance and to be an effective witness".
Mr Conlan insisted he was not responsible for his appointment or the €125,000 salary he was offered, which was in breach of HSE guidelines.
He said his salary was 48 per cent lower than his predecessor, Paul Kiely, who it emerged last night was in receipt of a massive pension top-up. Mr Kiely's top up is now under investigation by the HSE.
Mr Conlan said that he has since paid back any "excess salary" above the HSE approved salary level of €98,000.
He insisted that the awarding of the controversial top-ups were paid out with "full knowledge of the HSE arising from discussions between them and the Board chairman in July 2009".
He addressed the controversy surrounding the CRC Medical Devises, which was a seperate company set up in 2007 and which "was aimed at raising extra monies to support and develop CRC activities."
He said that a loan of 550,000 was taken from the Friends of CRC fund to begin the business of importing and customising wheelchairs for patients.
He said that by December 2012, losses of €462,000 had been racked up because of the downturn in the economy.
He added that on being appointed CEO last July he set about "sorting this matter out" and had agreed to sell the company for a price of €410,000, and will acknowledge the loss taken by the CRC.
Mr Conlan said he offered his resignation because of the "scale and nature of the coverage" and that he felt the "CRC was being damaged".
Daniel McConnell, Political Correspondent