BBC bosses blocked a Halifax school from singing an Arabic song at the televised final of the Songs of Praise Junior Choir of the Year Competition.
Parkinson Lane Community School had planned to sing In The Morning When We Wake – which repeatedly refers to Allah.
But the predominantly Muslim school fell foul of the rules requesting a "Christian-inspired song."
Head teacher Gugsy Ahmed was forced to compromise and his choir instead sang If You Pass Your Night, which is based on a poem by Muslim Poet, Rumi.
He said: "I didn't think we had fallen foul of the rules. The original song was celebrating the thought of God. Allah is an Arabic term for God and is referred to by many Arab Christians, in the same way that the word God is used by many British Muslims, and Dieu by the French.
"When we praise God, we praise one being, whether it's Christian, Islam, Judaism and so on."
Despite the original song winning the competition's selection rounds, the school was sent a letter – along with all other finalists – stating the rule for the televised final.
Mr Ahmed added: "The children represent a unified community in Halifax and we have Christians in the choir.
"It didn't spoil the overall experience for the children, they had a fabulous time."
The school went on to be named runners-up in the the national competition aired last Sunday.
The BBC confirmed it asked the school to change the song.
A spokeswoman said: "The rules of entry for the final were sent to all the schools chosen to compete.
"These clearly stated that song choices must be agreed with the competition organisers.
"The rules for the final stated that: 'The final of the competition will entail each choir singing one 'traditional' Christian hymn and one other Christian inspired song ie Gospel.'
"Parkinson Lane Community Primary School Choir's initial choice was not a Christian-inspired song, so they were advised to change it.
"The song If You Pass Your Night reflected the spirituality of the choir and was a choice that both the school and the BBC were happy with."
The Parkinson Lane choir will also feature on Songs of Praise on Sunday April 25 in a finalists' concert.