The highly offensive reference to God scrolled across the bottom of the screen during the end of year show, which also announced midnight at the wrong time and put out a spoiler for the new Star Wars: The Force Awakens film.
But criticism from L'Osservatore Romano, the Vatican-owned daily newspaper, was rebuffed by RAI board member Carlo Freccero, who said: "If anything is out of control, it's the Vatican, from what I read."
His comments were widely seen as a reference to new books exposing sleaze and mismanagement at the Holy See.
The New Year programme was being watched by nearly nine million people when it mistakenly announced the start of 2016 40 seconds early.
However, many suspect it was done deliberately to steal viewers from a rival channel, which is controlled by former Prime Minister Silvio Berlusconi and rang in the new year 20 seconds early last year.