The apology came from GPA spokesperson Kevin Boyle, in which he said it was "devastating" that some Christians were offended and he would "obviously offer apologies".
The advert, which appeared in the national press, claims that religiously motivated attacks against gay people have risen by 74 per cent in the last year.
The advertising standards agency has ruled the advert was offensive because it implied Christians were responsible for the surge in homophobic attacks.
The watchdog received over 500 complaints against the advert; the most received this year to date against a single campaign.
Despite the barrage of complaints, the GPA remains positive that its intended message may have reached some readers.
When asked if the GPA planned to continue producing similar adverts, Boyle commented, "Clearly it would be foolhardy to continue with an advert that had quite the same devastating effect on everybody."
The Rev George Hargreaves, leader of the Christian Party, is continuing his legal action against the GPA over the issue. He stated, "The whole issue has serious implications for the police force."
While Hargreaves is calling for senior figures at the GPA to be sacked, the GPA plans to launch an appeal against the rulings of the Advertising Standards Agency.
Boyle said, "We are disappointed that they [the ASA] have upheld various grounds of complaint, we are appealing against these grounds. We are a small group and are concerned by the assertion that we refused to comply with their request to submit evidence."