A lawsuit the church recently filed is seeking a court ruling that it doesn't owe the cash-strapped city the funds after it moved properties from one Catholic nonprofit corporation to another.
The taxes are collected when properties are sold or transferred to a separate and distinct legal entity.
San Francisco Assessor-Recorder Phil Ting contends the church not only owes the taxes, but also delinquency penalties and interest that bring the grand total to $21.7 million, according to the lawsuit filed Friday in San Francisco Superior Court.
In November, Transfer Tax Appeals Board unanimously ruled in Ting's favor on the dispute, but Maurice Healy, a spokesman for the archdiocese, has said that vote was tainted by political pressure from city leaders.
The city is trying to bridge a $483 million budget deficit, and the board is made up of the city controller, the city real estate director and the city tax collector, or their designees.
Ting on Monday rejected the idea that politics played a role.
"We have worked hard to ensure every taxpayer is being assessed transfer taxes in a fair and consistent manner," he said.
The spat has been simmering since the spring of 2008, when the archdiocese requested to change ownership titles of 232 parcels that city officials say are valued at close to $2 billion.
The properties involved range from churches like Mission Dolores to vacant lots to schools.
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