Scottish Church leaders have written to the UK Parliament to raise "grave" concerns over the Internal Market Bill.
In it, they warn that the passing of the legislation by Westminster "without the consent of the Scottish Parliament clearly strains the devolution settlement".
"The fracturing of an established relationship is in itself something to be regretted because it is vital that all levels of government work together in the interests of the communities we serve," the letter reads.
They echo a similar intervention last month by Anglican leaders who warned that the legislation would set a "disastrous precedent".
Peers are reviewing the legislation line by line ahead of a crunch vote in the Lords on 9 November.
The letter to parliamentarians has been signed by representatives of the Church of Scoltand, Roman Catholic Church, Scottish Episcopal Church, United Reformed Church, Methodists and Quakers.
They speak of concerns shared with them by Irish Christians who fear the creation of a hard border on the island that "puts in peril the delicate peace which has been built on the Good Friday Agreement".
"Since that document was signed Irish Christians have worked together to build better relationships across the communities," they say.
"Our brothers and sisters are deeply dismayed to think that so much of what has been done to heal the scars of past division will be torn apart by the re-establishing of frontiers. We wish to stand with them in their opposition to these divisive steps."
The letter ends with a warning that requiring royal assent would place the Queen "in the difficult position of having to sign legislation which breaks international law".