University President Richard Levin’s compensation reached seven figures for the first time in the 2007–’08 academic year, according to the University’s most recent tax filings.

But Levin was still only the fourth-highest paid employee at Yale. Topping the list, Chief Investment Officer David Swensen’s GRD ’80 salary and benefits amounted to $4.3 million, about twice what he made the year before.

Swensen’s deputy, Dean Takahashi ’80 SOM ’83, earned the second most, with $2.6 million in salaries and benefits, a 44 percent raise. Swensen’s and Takahashi’s exact earnings for the 2007–’08 year are difficult to pinpoint because their compensation includes deferred bonuses that they have not yet received as well as past deferred compensation, listed on previous tax filings, that they have now received; Takahashi called it “double counting.”

Most of Swensen’s and Takahashi’s compensation consists of incentive-based bonuses they receive on top of their base salaries, mostly tied to the long-term performance of Yale’s endowment. In the fiscal year ending in June 2008, the endowment grew a disappointing 4.5 percent.

Swensen’s and Takahashi’s pay trails that of their counterparts at the Harvard Management Company, some of whom have earned as much as $35 million in recent years. Yale outsources the direct investment of its endowment to external financial managers, whose pay is not publicly disclosed.

Swensen declined to comment.

David Leffell ’77, deputy dean of clinical affairs at the School of Medicine and a professor of dermatology, made $1.4 million last year; and obstetrics and gynecology professor Thomas Rutherford rounded out the top five with nearly $900,000 in salary and benefits. Leffell also declined to comment, and Rutherford did not respond to a request for comment.

Robert Alpern, dean of the School of Medicine, said market forces drive up salaries in parts of the University where professors could be making more in the private sector.

“If you go to the Law School or the School of Management, you’ll see salaries that are much higher than in the College because there are people who could be working on Wall Street,” Alpern said. “In the medical school you’ll find salaries that are higher because, for example, we have neurosurgeons who could be out in private practice.”

All medical school faculty salaries are determined within their respective departments, in accordance with the University’s guidelines, and then reviewed and approved by the dean.

Levin’s salary, which was $911,250 last year (plus $268,082 in benefits), is recommended by the three-person Compensation Committee of the Yale Corporation, the University’s highest governing body.

Federal law requires nonprofit organizations such as Yale to disclose annually the compensation of its officers and its five other highest-paid employees. Yale’s six officers besides Levin — the University’s secretary, general counsel, provost and vice presidents for New Haven and state affairs, development, and finance and administration — earned $432,500 on average in the 2007–’08 fiscal year.

Florence Dethy contributed reporting.