The company learned of the complaints through media reports and began direct talks with the church "yesterday or today," Sony Computer Entertainment spokeswoman Nanako Kato said in Tokyo.
"We take the church's views seriously," she said. She declined to give details of the talks.
More time may be needed for an agreement because the problem was complex, she said.
Historical buildings are often used in entertainment, she said, citing iconic movie scenes involving Godzilla and the Tokyo Tower and King Kong in Manhattan.
The church has said Sony Corp. did not ask for permission to use what appears to be Manchester Cathedral in scenes of the game and has demanded an apology.
Kato acknowledged the church in the game "Resistance: Fall of Man," a fast-paced first-person shooter, holds a resemblance in some parts to Manchester Cathedral. The point was to depict a backdrop of an old church, not to illustrate a specific church, she said.
In parts of the game, a character walks through a cathedral armed with a gun and shoots at alien enemies, which spew blood.
Although the cathedral appears only in some scenes, it would be difficult to delete just those scenes from the game, which went on sale with the launch of the PlayStation 3 next-generation console. The machine went on sale in Japan and the U.S. late last year, and in March in Europe.
Sony understands the Church of England was offended especially because of its efforts to reduce the serious problem of gun violence in Manchester, Kato said. She declined to comment whether Sony would donate money to such efforts.
Global sales of "Resistance: Fall of Man" — a Sony original — have totaled more than 2 million units, Kato said.