The external investigation report was prepared by a board chaired by the former Northern Ireland Ombudsman Dr Maurice Hayes and it was asked to make recommendations about RTE personnel involved in the programme.
The report is the last one to be completed in the wake of the Fr Reynolds affair.
In a statement RTE said: "The board has now concluded its investigation and has made a number of recommendations. RTE has accepted all the recommendations."
However, it said the investigation was convened "under RTE's procedures into all personnel matters arising in respect of the programme 'A Mission to Prey', and "these matters are confidential to the parties and accordingly RTE will not be make further comment."
A spokesperson added: "This now brings the personnel related matters arising from the 'Mission to Prey' programme to an end."
Defamation
Fr Reynolds said he did not wish to comment any further.
"I'm just trying to get back to a normal life. I would prefer now to remain quiet on that."
The other members of the external investigations board were Richard Ayre, who is one of a number of trustees with the BBC Trust where he chairs the Trust's Complaints and Appeals Committee, and Gaye Cunningham, who has has been a rights commissioner since 2008.
The programme resulted in a €200,000 fine being imposed on RTE by the Broadcasting Authority of Ireland and resulted in RTE reaching a settlement with Fr Reynolds who took a defamation case.
Ed Mulhall, the managing director of news and current affairs, retired and the reporter on the programme, Aoife Kavanagh, left RTE while Ken O'Shea resigned as editor of current affairs. Mr O'Shea continues to work for RTE.
The final report comes after what was a tough year for staff in RTE and as Kevin Bakhurst prepares to take over as managing director of news and current affairs in an organisation where morale was dramatically affected by the fallout from the programme.