By SCOTT THURM

Eli Lilly & Co. Chief Executive John Lechleiter received compensation of $20.9 million last year, up 45% from a year earlier, according to the formula the drug maker was required to use in its proxy statement. But Lilly thinks it is fairer to value the CEO's pay at $15.9 million, up 10%.

Executive pay is a hot topic, but the players can't agree how to keep score.

Pay controversies are sure to flare again in coming weeks, as hundreds of companies file their annual proxy statements. The math will look different, after the Securities and Exchange Commission changed its rules for calculating compensation for the second time in four years. Most experts say the changes are an improvement, but they might sow confusion.

Moreover, a growing number of companies, like Lilly, are presenting their own pay formulas alongside the SEC-mandated figures. The "summary compensation table" in Walt Disney Co.'s proxy says Chief Executive Robert Iger received total compensation of $29 million for the year ended Sept. 30, 2009. A few pages away, the same document says Mr. Iger received "total annual compensation" of $21.6 million.

To keep track of the numbers, "You need to be part accountant, part attorney and part archeologist," quips Brian Foley, a compensation consultant in White Plains, N.Y.

Executives are paid in varying amounts of salary, bonus, perks, stock, stock options and pension benefits. But most people tracking executive compensation—including directors, consultants, regulators and executives themselves—want to reduce each package to a single number.

That is hard when some payments are made in cash, while others are in stock, the value of which won't be known for years. For retirement benefits, the value might not be known for decades.

Mr. Foley notes that Goldman Sachs Group CEO Lloyd Blankfein and General Motors Co. CEO Edward E. Whitacre Jr. each received 2009 pay packages the companies value at roughly $9 million. Both were paid largely or exclusive in stock. But Mr. Blankfein's pay was deemed a reward for Goldman's strong profit last year, while Mr. Whitacre's was considered salary—in part to avoid restrictions on bonuses at companies receiving government aid. Either man's 2009 pay package ultimately could be worth $2 million, or $20 million, depending on future moves of Goldman and GM stock.

Even if the total pay for two CEOs looks alike, "you can pretty much bet they are not the same," Mr. Foley says.

Equity grants account for as much as to two-thirds of CEO pay, says University of Southern California business professor Kevin Murphy.

Valuing those equity grants has long bedeviled regulators. Until this year, the SEC required companies to calculate an executive's pay based on a formula that reflected all of the executive's outstanding stock grants, including those made in prior years. Most pay experts considered that number meaningless, because it didn't demonstrate how the company intended to reward the executive for the latest year.

The new rules count the value of the stock, or options, on the day they are granted, applying a widely used formula in the case of options. The changes are "an improvement on a flawed system," says Tim Bartl, senior vice president and general counsel of the Center on Executive Compensation, a business-backed research group.

Whatever the details, these approaches all attempt to put a value on compensation around the time it is paid, or granted. Mr. Murphy calls this "expected pay." But some analysts prefer to ignore stock grants and examine an executive's gains on previously granted stock. Mr. Murphy calls this "realized pay." (Even realized pay isn't necessarily money an executive puts in his pocket, because corporate officials in many cases don't immediately sell stock that has vested.)

The two approaches often yield different results. When Mr. Murphy calculated the 10 biggest 2008 paydays for executives under both systems, only five CEOs appeared on both lists.

Richard C. Adkerson, CEO of mining company Freeport McMoran Copper & Gold Inc., topped the expected pay list at $120 million, including a $66 million grant of restricted stock and a potential bonus valued at $43 million. (Mr. Adkerson declined any bonus, according to Freeport's proxy statement.)

On the realized-pay list, Mr. Adkerson ranked 16th, at $48.8 million. He was far outpaced by Occidental Petroleum Corp. CEO Ray Irani, who reaped $222 million, primarily by exercising stock options.

Mr. Murphy says the SEC's rules have changed repeatedly, often in response to a recent scandal. The agency required more disclosure about executive perks in the 1980s, after 1970s-era bribery revelations. The 1990s brought more details about stock options, after headlines about "mega-grants" that turned into $100 million paydays. More recently, the SEC added disclosures about pensions and post-retirement perks after the controversy around former New York Stock Exchange Chairman Richard Grasso.

The SEC says it changed the compensation-reporting rules in December "to better enable shareholders to evaluate" executives. The commission says grant values better reflect how directors intend to compensate executives.

Rules also can prompt changes in pay practices, often in unintended ways. A 1993 law that prohibited employers from deducting more than $1 million of an executive's annual salary prompted many companies to hand out more-easily deductible executive bonuses on a routine basis. Mr. Murphy calls these "sham" bonus plans that allow executives to be paid more than Congress intended.

Companies that list alternative pay formulas say they want to help investors by giving them more information. At Lilly, Dr. Lechleiter's 2009 compensation reflected an extra stock award, as the company shifted to a two-year bonus system from an annual system. The company also wanted to highlight how lower interest rates inflated the value of Dr. Lechleiter's pension. The $15.9 million total "we feel is more reflective of the compensation opportunity available" to the CEO, a Lilly spokesman says.

Disney says in its proxy that its additional calculations are "intended to provide additional information that the Company believes is useful in analyzing compensation decisions." A spokesman declines additional comment.

The SEC says it supports companies offering additional information, but not in ways that could confuse investors.

Any effort to reduce complex pay formulas to a single number likely is doomed, Mr. Foley says. Regulators "would love to have this be plug and play," he says, "but it is never going to be that simple."

Write to Scott Thurm at scott.thurm@wsj.com

Corrections & Amplifications
General Motors Co. Chief Executive Edward J. Whitacre Jr. will be paid $9 million, mostly in stock, in 2010. This column incorrectly says Mr. Whitacre's 2009 salary was $9 million. VF Corp. CEO Eric Wiseman received "expected pay" of $8.8 million in 2008. A chart that appears with the column misstated his expected pay as $60.1 million.