The program offers developers larger credits for building in poorer communities, which tend to need affordable housing the most but also have large minority populations. That has meant that even in a place like Houston, one of the country’s most diverse cities, racial divides can run deep.

When she got a federal housing voucher many years ago, Tonya McKinney said, she searched far and wide for an apartment but ended up in Houston’s Fifth Ward, a neighborhood she was not happy with. Founded by former slaves, the community, just east of downtown, has a long history of blight but has undergone significant redevelopment in recent years.

Her three children want change, she said.

“They talk about this all the time, about us moving into a better area,” said Ms. McKinney, 46, who used to work in retail but is now disabled. “They’re actually tired of living in what they call the ghetto.”

The proposed Houston housing, known as the Fountain View Drive project, would be built in the Galleria district, which sits a few miles west of downtown and features shiny office towers and stores. And at 87 percent white, it is an unlikely site for low-income tax-credit housing.

While only about a third of census tracts in the nation’s hundred largest metropolitan areas have a majority nonwhite population, 54 percent of new tax-credit projects have been built in those tracts since 2000, according to a Times analysis. And that pattern of placing tax-credit projects in communities with disproportionately high black and Latino populations has been consistent over time, the data shows.

The Treasury Department, which administers the program, includes no provisions in its regulations that address segregation. That, fair-housing advocates argue, runs afoul of the Fair Housing Act, which requires government agencies that administer housing programs to do so in a way that reduces racial segregation.

“It’s been clear for a long time that the tax-credit program is perpetuating racial segregation,” said Michael Daniel, a fair-housing lawyer.