The scarcity of female CEOs explains in part the S&P 500 gender gap. The small pool brings the average compensation down among women in the C-suite because chief executives tend to command the highest pay, said Ilene Lang, president of Catalyst, a New York-based research and advocacy group for women executives.

Chief executives are lagging behind their male counterparts in certain industries. Take Denise Morrison, CEO of Camden, New Jersey-based Campbell Soup Co.: She got total compensation of $8.76 million last year, 24 percent less than the average earned by CEOs at food, beverage and tobacco companies, according to data compiled by Bloomberg. Mylan Inc.’s Heather Bresch was paid $9.96 million, 33 percent less than the average chief of a pharmaceutical, biotechnology and life sciences company.

‘Large Gap’

“It is unfortunate that in many instances there is still a large pay gap between men and women in corporate executive positions,” said Maggie Wilderotter, 58, CEO of Frontier Communications Corp. since 2004 and a director at Procter & Gamble Co. and Xerox Corp. “I am hopeful that the use of outside compensation consultants by the compensation committees of public boards will make the gaps more evident and get inequalities addressed.”

Many factors contribute to pay levels, including performance, age and experience. Both Morrison, 59, and Bresch, 44, are relatively new in their CEO jobs, since August 2011 and January 2012, respectively.

There were 50 female chief financial officers ranked among the five highest-paid executives in S&P 500 companies last year. The lowest-paid was Karen Burns, Nvidia Corp.’s interim CFO since 2011; she received $841,517.

Kinder Morgan Inc. CFO Kimberly Dang, 43, has been in the job since 2005. Last year she got compensation of $1.72 million. Her Houston-based energy company had sales of $10 billion last year. By comparison, the average compensation of CFOs at five similar companies with sales ranging from $5 billion to $17 billion was $2.3 million.

Average Compensation

Mary Winston, 51, became chief financial officer at Family Dollar Stores Inc. in April last year after four years as CFO of Giant Eagle Inc., a closely held grocery chain with about $9 billion in sales. She got $1.1 million in compensation for the year ended August at Matthews, North Carolina-based Family Dollar, which had revenue of $9.3 billion in 2012. For fiscal 2013, she will make an estimated $1.3 million, if she hits her bonus target. The average CFO compensation at four discount retailers with sales ranging from $2.1 billion to $16 billion was $2.1 million last year, according to data from proxies.

Family Dollar, Kinder Morgan, Campbell and Canonsburg, Pennsylvania-based Mylan declined to comment.