For the first time, the IRS this year is requiring private colleges and universities and other nonprofits to factor in the value of certain nontaxable perks — such as the estimated fair-market rents of the housing many schools provide for presidents — in reporting executives’ total compensation packages.

The new rules, effective with the 2008 tax filings colleges submitted last month, aim to capture a more accurate and transparent picture of how top administrators are rewarded. But a Globe examination of the latest filings from 10 Greater Boston colleges shows a wide variation in how schools interpret the requirement.

In determining rental value, BU assessed the entire house, while other universities counted only the portion considered to be a private residence. The ground floor of a college president’s home often serves as public space for entertaining visiting dignitaries, faculty, students, and alumni. Brown himself describes where he lives as “an apartment over a restaurant,’’ since his home is used weekly for such university functions.

IRS instructions do not specify what portions of the homes should be counted in executives’ compensation, said BU spokesman Steve Burgay. “We just decided to err on the side of valuing the entirety of the house,’’ Burgay said. “No one likes to be at the top of that list, but it is what it is.’’

Local real estate specialists say many of the other presidential homes would fetch thousands of dollars more on the open market than schools have reported. One Boston realtor who specializes in luxury sales and rentals scoffed at Northeastern’s rental estimate for the house of its president, Joseph Aoun. “No, that would be more like $20,000 a month,’’ said the realtor, who spoke on condition of anonymity to avoid alienating university clients.

Another realtor, Tina Kaneb of Coldwell Banker in Cambridge, estimated the rental value of the MIT and Harvard residences at $12,000 a month each — a figure Harvard acknowledges in its tax filings would be accurate if the entire house were to be counted rather than just president Drew Faust’s private quarters.

“There are still areas that are open to interpretation as to what gets counted and what doesn’t,’’ said Richard Doherty, president and CEO of the Association of Independent Colleges and Universities in Massachusetts. “It gets a little tricky in terms of valuing housing. I think for the first few years, this will bounce around a bit.’’ ...

Then there’s the Boston College president, the Rev. William Leahy, who resides in simple quarters on campus in Saint Mary’s Hall, a Jesuit residence that the college says does not have a market value. Leahy also does not collect a salary, given the vow of poverty he has taken as a Jesuit priest, said a campus spokesman.

The IRS is in the midst of conducting an audit of more than 30 colleges and universities, including Harvard and Suffolk universities, focusing on executive compensation and analyzing possible reporting inconsistencies.