Producers of the BBC programme - broadcast on Tuesday night - were accused by senior Anglican figures of painting an inaccurate picture of the Lancashire town and overlooking the work of faith groups to promote community cohesion.
The Bishop of Blackburn, Rt Rev Julain Henderson said: "The Diocese and Cathedral didn't get the chance to take part in this documentary, so I urge the Panorama team to visit Blackburn again soon and tell the full story of what is happening here.
"We will be happy to speak to them."
The show, named 'White Fright', claimed that Blackburn is becoming increasingly segregated along ethnic and religious lines.
Intended as a follow-up to a programme aired in 2007 - which did feature Blackburn Cathedral - it featured interviews with various members of the community about the state of race relations in the town.
Anjum Anwar thinks "integration is about how do you live with the difference, not becoming the same". #BBCPanorama pic.twitter.com/Es1KO80diJ
— Panorama (@BBCPanorama) January 22, 2018
Bishop Julian, went on to say: "There are challenges of course, but Blackburn is not unique in that regard and we are involved in many initiatives where people from different backgrounds live, work, play and associate together."
"We engage together on topics of mutual interest at our active Anglican/Muslim forum."
The Bishop of Burnley Rt Rev Philip North added: "Blackburn also has numerous faith leaders, community leaders, councillors, teachers and activists who are passionate about cohesion and who are building bridges between communities.
What about segregation in young people? Ten years ago, Jaffer Hussein was a student - now he chairs a youth group to bring people from both communities together #BBCPanorama pic.twitter.com/OogGZTvqIz
— Panorama (@BBCPanorama) January 22, 2018
"It was a great pity that so few of these voices were heard in last night's documentary."
The Dean of Blackburn, Very Rev Peter Howell-Jones: "Engagement with our Muslim neighbours in the town is straightforward and the Cathedral itself is at the centre of driving forward community cohesion work, with initiatives such as our Cathedral/Mosque programme which brings together young people from our schools to create better understanding of our faiths.
"We will continue to work closely with our Muslim neighbours and those from other faiths in the years to come."
Premier has contacted the BBC for a response.
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