The report by GMI Ratings showed Zuckerberg's salary of $503,000 and bonus of $266,000 were eclipsed by stock options worth some $2.27 billion.
This was the first year the survey found any chief executive collected more than $1 billion, according to the GMI report released yesterday.
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Those two overshadowed other CEOs, with the third-highest paid being Sirius XM Radio's Mel Karmazin at $255 million, followed by Liberty Media's Gregory Maffei ($254 million) and Apple's Tim Cook ($143 million).
Maffei also collected $136 million for his role of CEO at Liberty Interactive Corp, the seventh highest on the list. Putting those two together would make him the third highest-paid with $390 million.
In the survey of 2,259 North American publicly traded companies, GMI said pay increased a median of 8.47%. For the companies in the Standard and Poor's 500 index, compensation rose 19.65% at the median.
"In the more than ten years that GMI has been publishing this report, I've never seen a top ten highest paid list that loomed this large," said Greg Ruel, report's author.
"While the companies in this year's list have performed well over the past three and five year periods in terms of shareholder return, generally speaking, it's the sheer size and volume of equity awards granted to these top executives that catapults their total compensation to astronomical levels."
The massive compensation packages are generally due to stock awards, often in the form of options which allow a CEO to buy shares at a fixed price and cash in on gains.
GMI said Zuckerberg exercised 60 million stock options, granted in 2005 and fully vested by 2010, at a strike price of just six cents.
When Facebook went public in May 2012, Zuckerberg's worth vaulted by more than $2.7 billion dollars on the difference.
"Lest anyone think these are merely paper profits, readers may recall that Zuckerberg immediately liquidated more than $1 billion worth of shares at the company's IPO," the GMI report said.
"The second largest form of compensation for Mr Zuckerberg was perquisites totaling about $1.2 million, including personal use of company aircraft during 2012 for him and guests as well as security costs."
The others in the top 10 list were Dick's Sporting Goods's CEO Edward Stack, paid $142 million, Starbucks' Howard Schultz ($117 million), Salesforce's Marc Benioff ($109 million) and Verisk Analytics' Frank Coyne ($100 million).
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