RTE management has protested to the Minister for Agriculture at his remarks about journalist Charlie Bird.
An emergency meeting of the RTE newsroom chapel (section of the National Union of Journalists) called on Mr Yates to withdraw the comments unreservedly.
As RTE's Special Correspondent Mr Bird has been following the campaign of the Fianna Fail leader, Mr Bertie Ahern. On Sunday night's Questions and Answers Mr Yates claimed that Mr Ahern was doing a "soft shoe shuffle" with "video promotional material from Charlie Bird".
Amid criticism from other panel lists on the programme, Mr Yates went on to say that no hard questions were being asked about the Progressive Democrats' proposals to cut 25,000 jobs in the public service.
The union meeting condemned "the attempt to drag the name and reputation of a journalist into political debate".
A motion commending Mr Bird as a journalist of the highest integrity and professionalism, who has carried out his duties "in an unbiased and rigorous fashion in this election campaign as in any other", rejected the Minister's remarks and called on him to withdraw them.
Copies of the motion were sent to Mr Yates and to the Fine Gael press office.
Following a complaint about the Minister's remarks to the Fine Gael press office, Mr Yates is understood to have telephoned Mr Bird and apologised. The NUJ, however, is insistent that the Minister make his apology and retraction public.
The NUJ meeting also noted "with concern" comments in the Sunday Times about journalist, Joe O'Brien, attributed to Fine Gael staff. Mr O'Brien is assigned to the Taoiseach's campaign.