The Scottish Government's punchy 'Dear Haters' series last year included a 'Dear Bigots poster', with one version stating: "Dear Bigots, you can't spread your religious hate here. End of sermon.
"Yours, Scotland."
The Evangelical Alliance (EA) said many of its members as a result were "worried that they, as people of faith, were being accused of being hateful, rather than being protected from hate crime".
The Christian group encouraged people living in Scotland to contact their MSP to highlight the potential negative effects of the campaign.
EA also wrote to Humza Yousaf, the cabinet secretary for Justice, and Aileen Campbell, the cabinet secretary for Communities and Local Government, about the issue.
Campbell apologised and replied: "I would like to confirm that the poster was absolutely not intended to target those of faith, and I am sorry if it appeared that it did.
"We have no plans to reuse this poster in the future.
"I would also like to reassure you that this government values our relationships with our Christian communities and appreciates the valuable contributions they make to Scottish society, including supporting many of our most vulnerable and disadvantaged communities."
The EA has welcomed the "positive response as a step forward in building better discussions between ourselves, our members and government".
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