Harvard University’s endowment chief, Jane Mendillo, earned $3.5 million in 2010, down from $4.8 million in total compensation in 2009, according to Harvard, which released its latest tax filing Friday.

The highest paid manager of the endowment in 2010 was Andy Wiltshire, who earned $5.5 million, Harvard said, for overseeing the outside firms that manage money for the nation’s largest endowment. Harvard’s top investment managers are highly compensated, routinely earning more than anyone else at the university if they beat their goals.

The university’s president, Drew Gilpin Faust, earned $875,331 in 2010, up slightly from $874,559 the prior year. For 2010, $120,901 of Faust’s compensation was for the personal use of the president’s house in Cambridge.

Harvard’s tax filing was for the fiscal year that ended June 30, 2011, but the compensation figures it disclosed are for the prior calendar year.

Mendillo’s pay was lower compared to 2009, which included deferred compensation that was part of her employment agreement. Mendillo rejoined Harvard in 2008 from Wellesley College, where she also managed the endowment.

Mendillo has been working to improve the performance of the Harvard endowment after double-digit declines in the financial crisis of 2008 and 2009. She oversaw a 21.4 percent return on the $32 billion endowment in the 12 months ended in June 2011, slightly better than the 20.1 percent average gain among all endowments larger than $1 billion that year.

The high pay of Harvard’s investment managers has long been a source of debate on campus and among some alumni. Proponents of the pay structure say this is how the endowment attracts top investment talent.

Over the years, a number of Harvard managers left to start their own hedge funds, in part to avoid the annual scrutiny of their pay. Those managers continue to handle billions of dollars for the endowment, only now their compensation is generally not disclosed. In 2009, one of those firms, Regiment Capital Management, was one of Harvard’s five highest-paid contractors, receiving $19.2 million in fees.

James F. Rothenberg, Harvard’s treasurer and chairman of the endowment board, said Mendillo and her team “continue to steer the endowment through challenging markets, returning value to the portfolio and the university while positioning Harvard’s endowment for the long term.”