According to the Daily Mail, helpers from the Noah's Ark group in Burgess Hill would visit the town's library in The Martlets once a month to sing songs about Bible stories.
But West Sussex County Council decided to stop them singing at the rhyme time sessions after complaints that the children were singing about God, according to the Mail.
The songs included 'Mr Noah Built An Ark', to the tune of 'Old MacDonald Had a Farm'.
A spokesman for the council explained the decision.
They said: "Rhyme time sessions are held every week in all West Sussex libraries and are open to everyone including families of any faith or no faith.
"In Burgess Hill a partnership was formed with a local faith group some years ago before rhyme time sessions were offered across all libraries.
"We have been very grateful to this group for their support but following feedback from families, we have decided to bring these sessions in line with the other rhyme times in our libraries which are led by staff.
"Families can continue to access faith-based activities in community venues and library staff are very happy to help anyone looking for details of where they can join these."