Sony has issued an "unreserved" apology to Manchester Cathedral for using the location as a violent backdrop in Insomniac's Resistance: Fall of Man.
The game features the place of worship in one of its many levels. When the Church of England found out a month ago it threatened legal action.
Although Sony published an apology in a city newspaper, it has confirmed it will not be withdrawing the game or making any changes to it.
Cathedral Dean, the Very Rev Roger Govender, said that he still feared another religious building could be "cloned for virtual desecration".
The Sony apology, in the Manchester Evening News, followed a meeting between the cathedral and the firm.
Dr David A Reeves, president of Sony Computer Entertainment Europe, said: "It is clear to us that the connection between the congregation and the cathedral is a deeply personal and spiritual one.
"As a result, it is also clear that we have offended some of the congregation by using the cathedral in our science fiction game.
"It was never our intention to offend anyone in the making of this game, and we would like to apologise unreservedly to them for causing that offence, and to all parts of the community who we might also have offended."
Dr Reeves also said the firm would ensure that Manchester Cathedral was not used in any of its games again.
The Dean said: "We asked Sony to withdraw the game. They have refused to do this.
"We asked Sony to make a substantial donation to community groups nominated by the Cathedral. They have refused to do this.
"We also asked them to sign up to the Sacred Digital Guidelines. They have refused to do this."
"We fear that the next buildings to be cloned for virtual desecration could be a mosque, synagogue, temple or other churches."
