NSS said the episode, which included an interview with Archbishop of Canterbury, Most Rev Justin Welby, amounted to a "PR exercise for the Church of England".
NSS chief executive Stephen Evans wrote: "The bias and deference towards the Church of England demonstrated in this show suggests a 'cosy relationship' has developed between the BBC and the Church, which undermines public confidence in the BBC's commitment to impartiality."
The episode was broadcast on 14th December from Lambeth Palace, which is the Archbishop Justin's residence.
Great to have @BBCr4today broadcast from @LambethPalace today. Especially good to hear so many stories of how churches are out there serving communities, supporting the vulnerable and sharing the love of Jesus Christ. It's what we do. #r4today pic.twitter.com/OtdPYq7umi
— Archbishop of Canterbury (@JustinWelby) December 14, 2017
The show included a performance from a Westminster Abbey choir, the Bishop of Manchester speaking about the Church's ethical investment fund and Archbishop Justin's chaplain reflecting on the Grenfell Tower fire six months on.
The Today programme will be broadcast live from @LambethPalace tomorrow morning. Listen from 6-9am to hear Archbishop of Canterbury @JustinWelby, @BishManchester, @BishopNewcastle, @YearInGodsTime and more. #r4today @BBCr4today pic.twitter.com/YjNrWq3x7c
— Lambeth Palace ن (@lambethpalace) December 13, 2017
The NSS added the episode was inappropriate in light of the Church's "ongoing official Independent Inquiry into Child Sex Abuse".
It group said in a statement: "The show frequently portrayed the Church in a positive light, with no opposing, critical views given... absolutely no reference was made of the sex abuse scandals or other controversies surrounding the Church."
The group's criticism comes a day after the BBC promised to do better religious broadcasting by portraying the diversity of beliefs and society without letting Christianity in programming suffer.
