An atheist organisation has filed a brief in court supporting a city's decision to tax a vacant Catholic Church property in Madison, Wisconsin.

In a brief filed with the Dane County Circuit Court Branch 16, the Freedom From Religion Foundation (FFRF) said the St. Raphael's Congregation should not be exempted from paying property tax on a lot that was the former site of a cathedral that burned down in 2005.

The church filed a lawsuit against Madison City last year to recover more than $98,000 in taxes it paid in 2014 on a lot in downtown Madison that has been assessed to cost more than $4 million.

Circuit Court Judge Rhonda Lanford issued a ruling on June 27 allowing FFRF to file a brief.

FFRF said since the lot is vacant and is being held for future development, St. Raphael cannot qualify for a tax exemption under Wisconsin law.

The Catholic Church put up a Way of the Cross on the lot to commemorate Christ's path to crucifixion and to show it is using the property, The Cap Times reports.

"That shows continued religious use," said lawyer Matthew Fleming, who's representing the congregation. "It shows it's continuing to still be held for the cathedral. But I also still believe that because the property continues to be held and reserved for the purpose of one day constructing a new cathedral for the Madison diocese, that that also provides additional grounds for continuing the exemption."

Besides the former site of a cathedral, the land used to host a school building that the church bought in 2011 and torn down in 2012.

Madison started taxing the church for the property in 2012.

St. Raphael said the property will be used to build a $50 million cathedral in the future.

"All Madison taxpayers should not have to pay more taxes while St. Raphael's invests in its other property holdings in Madison and holds the St. Raphael's lot for future development," said FFRF staff lawyer Patrick Elliott wrote. "It is precisely for this reason that property must be used to maintain an exemption."

St. Raphael's lawyer said in court documents that "the Madison Diocese is faced with the daunting task of raising an estimated $50 million for the project amidst the Diocese's other pressing financial obligations and needs" such as building a student apartment at another church property.

"The church's sense of entitlement to a tax exemption is astounding," said FFRF co-president Annie Laurie Gaylor. "Municipalities must tax religious properties that are not being used for that purpose, to demonstrate to taxpayers that church holdings are not being given special preference."

Madison and St. Raphael have submitted motions for summary judgment on the matter.