Taoiseach Enda Kenny has said RTÉ had to consider the costs of litigation when deciding to pay out €85,000 in relation to the broadcast on alleged homophobia.
Earlier this week, RTÉ confirmed that it had paid a total settlement of €85,000; €45,000 to members of the Iona Institute and €40,000 to journalist John Waters following the use of the word "homophobia" on the Saturday Night Show.
When asked if RTÉ should have made the payment Mr Kenny said: "I don't speak for RTE. Obviously litigation is an exceptionally costly measure.”
"RTE have said they've examined all of this [and] in the interests of the situation that they saw, they've made these payments.
"That doesn't mean you shouldn't have the opportunity for a free and open conversation about issues that affect people."
Mr Kenny said he hoped that in next year's referendum on gay marriage there would be a "thorough, comprehensive and fair debate" on the issue.
Earlier today, Mr Waters disputed a statement made by RTÉ on the settlement made with him.
However, RTÉ insisted it provided a fair and accurate account of the negotiations.
RTÉ said in reaching the decision to settle, it had explored every option available to it including right to reply.
It said that legal advice had been sought and all avenues explored, including an offer to make a donation to a neutral charity.
This morning a solicitor representing Mr Waters, Kevin Brophy, issued a statement saying RTÉ's statement was a "grossly misleading version of what had actually happened".
The statement goes on to say that Mr Waters had proposed the precise wording of an apology and further proposed that a donation of €15,000 be made to the St Vincent De Paul, however RTÉ was not happy to broadcast the apology as drafted.
Mr Brophy said that RTÉ believed that €5,000 should be paid to SVP and he said his strong advice to Mr Waters was to issue proceedings against RTÉ as he did not believe they were taking the matter seriously.
Finally RTÉ offered €40,000 and this was accepted.
RTÉ responded this afternoon saying it stands by its previous statement.
It said it provided a fair and accurate account of the negotiations and their conclusions, and that the apology proposed by Mr Waters was unacceptable to RTÉ.
The broadcaster said it is untrue to claim that RTÉ did not take all matters relating to the complaint seriously from the outset.