UPDATED: May 16, 2014, at 10:23 p.m.

University President Drew G. Faust received a total compensation package of just over $1 million in 2012. according to a recent University filing with the Internal Revenue Service. In 2011, Faust earned $899,734 after benefits.

With benefits, Faust earned $1,040,637 during the twelve-month span. The bump in compensation stems mostly from a raise in Faust’s non-salary benefits, which include the presidential residence at 33 Elmwood Ave.  in Cambridge. Faust’s pre-benefit compensation rose from $729,106 to $770,887 from 2011 to 2012. Additionally, Faust earned a $75,000 salary and $175,000 in stock options for serving on the board of Staples, Inc.

While Faust was the highest earning University administrator, she was out-earned by numerous officials within Harvard Management Company. In 2012, HMC President and CEO Jane L. Mendillo earned $4,801,347—a decrease of more than $500,000 from 2011—while Andrew G. Wiltshire, head of alternative assets for HMC, was the company’s top breadwinner with $7,896,277 in compensation.

HMC employs a performance-based compensation system linked to overall market performance, according to the company’s announcement.

Five officials at HMC, including natural resources portfolio manager Alvaro Aguirre-Simunovic, head of public markets Stephen Blyth, and real estate portfolio manager Daniel W. Cummings, earned more than $4 million in 2012.

The filing, IRS Form 990, is required by all tax-exempt organizations, and lists the compensation of University officers and other top earners. Provost Alan M. Garber ’76 was the most highly compensated administrator after Faust, earning reportable compensation of $619,093 and a total package of $750,885. The most highly compensated dean was Jeffrey S. Flier of Harvard Medical School, who earned $582,243.

Much of the non-salary compensation for Faust and Garber, as well as Harvard Business School Dean Nitin Nohria and Dean of the Faculty of Arts and Sciences Michael D. Smith, came in the form of a University-owned residence or, in Smith’s case, a housing allowance. With benefits, Smith earned $554,370 in 2012, while Nohria received a total package of $681,073.

Other notable pay packages included a salary and benefits total of $447,910 for Christine M. Heenan, vice president for government communications and public affairs. Vice President for Alumni Affairs and Development Tamara E. Rogers earned a total of $410,978, during the “quiet phase” of the University’s ongoing capital campaign. Steven E. Hyman, the former provost and current chair of a task force convened by Faust this April to develop recommendations for policies aimed at preventing sexual assault on campus, earned a package of $497,416 during the span. Because of a one-time lump sum payment negotiated in 1987, Economics professor Amartya Sen, who earned a base compensation of $303,450, received a total package of $1,234,998.

—Staff writer Matthew Q. Clarida can be reached at matthew.clarida@thecrimson.com Follow him on Twitter @MattClarida.

This article has been revised to reflect the following correction:

CORRECTION: May 16, 2014

An earlier version of this article incorrectly stated that compensation packages for Harvard administrators were reported for June 1, 2012-June 30, 2013. In fact, those figures are for their compensation during the 2012 calendar year.