Fighting City Hall has turned out to be a rather expensive proposition for the owners of some struggling downtown Boston office buildings.

City Hall has slapped developers and other real estate types with anywhere from a few hundred to hundreds of thousands of dollars in financial penalties after they appealed tax assessments on often half-empty buildings.

Now a top Boston elected official has launched his own investigation to get to the bottom of the mysterious tax bill increases that some building owners have been hit with.

City Councilor Ed Flynn has filed a 17F order requiring the Wu administration to cough up information on the controversial and seemingly newfound practice of penalizing property owners who appeal their tax assessments.

“There have been a series of reports in the media expressing concerns about assessing practices in the City of Boston, specifically as it relates to the assessment of office towers,” Flynn notes in his order.

The label “ATB dispute” was affixed to the city tax records of the properties in question. Short for the state’s Appellate Tax Board, the ultimate authority on tax appeals, according to Daniel Swift, a top Boston tax whose sleuthing on behalf of his clients uncovered the charges.

City officials then hiked the tax assessments on the buildings in question, triggering higher tax bills.

Swift contends the penalties were hidden, noting he only spotted them when examining paper tax documents for various buildings that had been filed at City Hall.

In a recent interview, Swift called the penalties “shocking,” saying he had never seen anything like it in all his years of work representing city building owners.

For his part, Flynn is seeking a list of all buildings that city officials have affixed the costly “ATB dispute” label to the rules regarding the use of the penalties by city officials, and what records are kept on them.

Flynn, to substantiate his Request for Information from the city, mentions Boston’s history in the 1970s of over-assessing and hence overtaxing office and commercial buildings, which led to a $140 million court judgment.

In today’s dollars, that would amount to $620 million, Flynn noted.

The Boston Policy Institute (BPI) has warned that the city could face the loss of anywhere from $1.4 billion in tax revenue in the best case scenario to more than $2 billion in the worst over the next few years, amid the collapse of office tower values following the shift to remote work.

“This current dispute over assessment practices has a real back-to-the-future flavor that should be familiar and frightening for anyone who knows Boston’s history,” Greg Maynard, executive director of BPI, noted.

Scott van Voorhis is a longtime Boston reporter specializing in real estate and is the publisher of Contrarian Boston.