The Communications Clinic, where Mr Savage is a director, worked for the IMU before the broadcast to prepare its members for a planned expose by RTÉ.
Mr Savage’s wife and co-director of the Communications Clinic, Terry Prone, denied this had presented a conflict of interest.
Ms Prone said she was asked by the IMU to advise its members on one specific aspect of the programme, where a number of orders required a response.
This involved one meeting between her and the IMU and it was well ahead of the broadcast of the Prime Time Investigates A Mission to Prey programme, she said. This programme subsequently and sensationally defamed Galway priest Fr Kevin Reynolds.
RTÉ has said Mr Savage had not been made aware of the content of the programme prior to its broadcast because this would have been dealt with by its news division.
It also said he would not have known about specific issues arising from it, as they affected RTÉ, until four months later.
And RTÉ said Mr Savage had confirmed the statement by Ms Prone that he had been told about her work with the missionary union.
Ms Prone said she did not work for the orders on this issue after the broadcast.
She said the missionary union had specifically asked for her when it looked for advice before the piece aired in May 2011.
And she said she did not discuss it with Mr Savage or anybody else in the company, as it was not practice to do so where sensitive issues were involved.
The position of the Communications Clinic has been questioned by Labour Party senator John Whelan.
He said because of Mr Savage’s business interests, he was not an “appropriate” appointment as chair of the State broadcaster.
Mr Whelan said he could not accept that Mr Savage would not have been aware of the work being done for the Irish Missionary Union as he was the co-owner and director of the Communications Clinic.
“This is quite a substantial development. It is at odds with what Mr Savage advised the [Oireachtas] committee last week and it is a clear and unfortunate example of the type of conflict of interest I referred to.”
The comments came after broadsheet.ie pointed to an IMU strategy document published the week prior to the Prime Time Investigates programme. This referenced the preparation for its planned response to the RTÉ “expose”.
Mr Savage has denied there had been any conflict of interest between his work with the Communications Clinic and his role as chairman of RTÉ.