A Dorchester pastor is contesting a $48,380 tax bill from the city of Boston for several of his properties, saying the sum could cripple his Catholic parish. The properties include the former St. Kevin’s Parish property in Uphams Corner, which is in the midst of being converted into affordable housing for families, and two parcels on the St. Peter’s Parish campus on Bowdoin St.

They are among a number of church properties that the city’s Assessing department has deemed vacant this year and, thus, no longer falling under tax-exempt status. Around 50 percent of Boston’s properties are considered tax-exempt, because of the high number of nonprofits, such as churches, colleges and hospitals, among others, that own land in the city.

Fr. Jack Ahern, who oversees the tri-parish that includes St. Peter’s, Blessed Mother Teresa and St. Kevin’s, understands that the city is strapped for cash. But he says that the parishes can’t afford to pay the tax bill, which covers the third quarter, and he may have to cut back on services if he is forced to pay.

“It’s just taking from the poor,” Ahern said. “Both of those parishes are very poor. And we serve very poor populations.”

Ahern has applied for a tax abatement, but plans to pay the tax bill for now with money he has in reserve and funds he would normally be using for parish activities.

“It would be difficult for either of those parishes to pay that type of bill and continue to remain open,” he said.

Ahern said the properties should not be declared vacant, because church activities have still been occurring in them. At the St. Peter’s properties, there is a weekly flea market and baptismal preparations.

And Ahern notes that the St. Kevin’s property, which closed in 2008 as part of a church consolidation plan, will soon be back on city tax rolls, once permits for the affordable housing project are approved.

The St. Mary’s Women and Children’s Center, the Holy Family Parish, and a nonprofit real estate developer with ties to the Boston Archdiocese’s Planning Office of Urban Affairs are working on the project.Ahern said he is working with Mayor Thomas Menino’s office on a solution, adding that city officials have been responsive. Ahern has worked with Menino’s office on other issues, such as curbing gun violence in the neighborhood.

Menino spokeswoman Dot Joyce said the mayor believes the parishes should not be hit with tax bills if the properties are performing a nonprofit function. The tax bills are now under review by a board within the city’s assessing department. Staffers have 90 days to review the abatement application and make a recommendation to the board. If Fr. Ahern disagrees with that ruling, he can appeal to the state appellate tax board.

“This is one of those issues where this is not something we have a great deal of choice over,” said Ron Rakow, the city’s assessing commissioner. “The law is pretty clear about what we have to exempt and what we have to tax.”

He said the process of determining whether the properties are vacant was “pretty thorough,” with field inspections of the parcels. But he added that if there are uses or activities happening on the properties that the department wasn’t aware of, they’re “willing to listen.”