St. Paul city officials are denying a church’s allegations that their historic building was demolished in 2009 to make way for the Green Line light rail.

Deputy City Attorney Jerry Hendrickson said the city has not been formally served with the civil complaint, which was filed Wednesday in U.S. District Court on behalf of 100 parishioners at Rock of Ages Missionary Baptist Church. The predominantly black congregation owned St. Matthew’s Church, a gothic revival-style brown brick building with a tall steeple and stained-glass windows in St. Paul’s Frogtown neighborhood.

Severe water damage forced the congregation to begin worshiping elsewhere and the group was unable to afford major renovations. The church, built by German immigrants in 1888, was torn down after sitting vacant for four years.

City officials dispute the fact that the building was an officially designated historic site, as the church claims, and vehemently deny having an ulterior motive for removing the structure.

“The building was not demolished for the Green Line light rail project,” Hendrickson wrote in an e-mail to the Star Tribune. “It was demolished because it was a public nuisance due to its dangerously dilapidated condition. The church did not legally challenge the demolition at the time.”

Rock of Ages also contends that the city’s demolition contract included a provision that the subcontractor could remove and sell any objects of value, regardless of whether parishioners wanted them back. Stained-glass windows, church pews and a cherished bronze church bell all were sold without permission, documents allege.