The programme has come under criticism for taking its cameras to a makeshift church at the centre of the camp.
"It is not a political statement on the situation or a judgement on migration," said the BBC's head of religion and ethics, Aaqil Ahmed, in a blog post.
"To suggest so is wrong."
He added: "Songs of Praise is not only about Christian music, it also explores contemporary issues and modern themes from a Christian perspective."
Thousands of migrants from countries including Syria, Libya and Eritrea are camped in and around Calais. Two sections of Songs of Praise, which will be broadcast on Sunday, have been filmed at the camp.
The Daily Express and The Sun were among newspapers which criticised the BBC's decision to film at the camp.
The Sun wrote: "The BBC sending Songs of Praise to the Calais migrant camp amid the current chaos is like something from Monty Python.
"Will we get to see migrants wrestling with riot police and storming lorries as a choir stands at the Channel tunnel welcoming them with a rousing rendition of Jerusalem?"
Prominent figures from the Church of England have defended the programme including the Archbishop of Canterbury Justin Welby, who tweeted: "The love of Christ is freely offered to all, celebrated everywhere, for everyone to know, well done #SongsOfPraise and @giles_fraser"
The Dean of Durham, Decanus Borealis, wrote in a blog: "I'm glad that SOP can be there to give the migrants air-time in a broadcast forum where it would be so easy to pretend they don't exist."
Mr Ahmed said, in his BBC blog: "The knowledge that the migrants had built a makeshift church is exactly the kind of action that Christian communities everywhere will relate to."
"Songs of Praise is simply reflecting the conversations going on in many churches and Christian households around the country.
Songs of Praise is on Sunday 16 August at 17:00 BST on BBC One.
The BBC has defended filming a Songs of Praise episode at a Calais migrant camp saying it is "reflecting conversations going on in Christian households".