In the kinds of incentive plans becoming more popular, executives do not receive higher compensation just because a company's share price rises, but rather must perform well on a series of measures—not just profit, but often including revenue, margins, cash flow, and in some cases even a company's safety and environment records.
"They're not going to get monster rewards," said Alan Johnson, managing director of pay consulting firm Johnson Associates in New York. "The indications are that companies continue to do a better job of matching up pay with performance."
However, the figures are unlikely to assuage concerns that CEOs are reaping bigger increases than those received by many Americans further down the food chain, exacerbating inequality. President Barack Obama has been stressing policies intended to reduce inequality, such as a push for a higher minimum wage.
(Read more: BofA executives' pay rose 12 percent in 2013)
The study looks at what was granted to CEOs for 2013 and does not include all the compensation CEOs actually pocketed in 2013 after stock and option awards granted to them in previous years were exercised or vested. With the S&P 500 surging 32.4 percent last year, including dividends, and almost tripling from the lows it hit in the financial crisis, some of those awards from 2009-2012 have proven very lucrative.
A separate review by executive compensation data firm Equilar of 44 companies in the Fortune 1,000 that filed their statements in January or February shows that the median value executives gained from exercising stock options or stock vesting was $2.1 million in 2013, up 18 percent from 2012.
Investor activists and proxy advisers, including ISS, have pressed companies for years to align pay with shareholder interests. In recent weeks, a handful of companies have made radical changes in the way they reward their CEOs, including semiconductor maker Intel and mining group Freeport-McMoRan Copper & Gold.
Among the 46 S&P 500 companies surveyed, the median cash salary rose $27,584, or 2.6 percent, to $1,079,327. But the median stock award rose $337,493, or 9.5 percent, to $3,887,008, and the median cash incentive award rose $63,799, or 3.3 percent, to $1,998,102.
Restraining the overall increase, though, were less generous stock options awards. Of the 46 companies, only 32 of them awarded stock options to their CEOs in 2013, down from 35 in 2012. For those 35 companies (including those who did not grant options in 2013), the average award fell by $548,543, or 23 percent, to $1,880,476 in 2013.
Some companies said they reduced their option awards as they wanted to reduce the incentive to take certain risks. At financial services company Comerica, total compensation for CEO Ralph Babb fell 10 percent to $6.46 million, as the value of his option awards fell to $314,729 from $1,047,682 in 2012. Comerica said in a filing it cut the weighting of stock option awards during the year to "discourage inappropriate risk taking and better align with regulatory expectations."
At paint maker Sherwin-Williams, total compensation for CEO Christopher Connor fell 1.5 percent to $10.8 million, as the value of stock option awards fell to $3 million from $3.3 million in 2012. The company said in a filing that it has de-emphasized stock options in favor of stock awards related to performance to provide more focus on operating performance.
(Read more: Chart of the Day: Bank CEO pay on the rise)