Princeton University, for example, pays $1.2 million voluntarily to the Borough of Princeton, and $500,000 to the township. But when the university met resistance from local officials this year to some zoning changes it is seeking to build a new $300 million arts complex — especially to its proposal to move a train station a little farther from downtown — university officials said that they might rethink those voluntary payments.

“It would be difficult to justify continuing contributions at existing levels to local officials who not only refuse to help the university achieve a key educational objective, but in some cases have sought to prevent the project from going forward,” Robert K. Durkee, the university’s vice president and secretary, said in an e-mail, adding that the university already pays taxes on some properties that could qualify for exemptions, including housing for graduate students.

Boston is trying to avoid those kinds of negotiations by making its payments more systematic — an approach other cities are watching closely.

Boston is sometimes known as the Athens of America for its universities, and its hospitals and museums draw visitors from around the world. As the capital of Massachusetts, it is home to many government buildings, from the golden-domed State House atop Beacon Hill to the most obscure agencies. But there is a downside to all that activity, which is so central to the city’s character: it leaves more than half of Boston’s land exempt from property taxes, said Ronald W. Rakow, the city’s commissioner of assessing.

While Boston has long collected voluntary payments from its nonprofit institutions, it has done so haphazardly, with some universities paying millions of dollars, while their peers paid little or nothing. So Boston’s mayor, Thomas M. Menino, convened a task force that studied the issue for much of last year and decided to try to establish guidelines for the voluntary payments. This year the city is trying to collect voluntary payments from all nonprofits with property worth more than $15 million. The payments will eventually rise to a quarter of what the nonprofits would pay in property taxes if they were taxable, with the provision that they can get credit for up to half of the money they owe by providing quantifiable “community benefits” that directly help city residents. By the time the system is phased in, the city hopes its annual payments from nonprofits will rise to $48 million from $15 million.

“There are some institutions that have already signed on to the program,” Mr. Rakow said. “Others are taking a wait-and-see approach.”

A study last year by the Lincoln Institute of Land Policy, a research institute in Cambridge, found that the voluntary payments had already been made in at least 117 municipalities in at least 18 states. But Daphne A. Kenyon, a visiting fellow at the institute who was an author of the report, said more cities were expressing interest in such payments as the fiscal crisis had continued, views of nonprofits had evolved and the antitax climate had grown more pronounced in many places.

“I think the most important conclusion is that this should be a collaborative process,” Ms. Kenyon said. “Because if you don’t make it collaborative — if it’s highly contentious, you could end up with no increase in revenue for the municipalities, a lot of legal bills and a lot of ill will.”