The chief executive of Dean Foods Co.'s pay plunged 42% last year as the company grappled with persistent challenges in the milk industry.

Dean CEO Gregg Tanner received $3.7 million in total compensation, including stock awards and other payments, in 2013, down from $6.4 million a year earlier, according to an annual proxy filing Friday with the U.S. Securities and Exchange Commission.

Other senior Dean executives also received lower compensation last year, according to the filing.

Dean's stock price fell 47% last year as the largest U.S. milk processor by sales struggled to manage the rising cost of raw milk and consumers' reduced appetite for dairy-based beverages. The Dallas company also suffered the loss last year of Wal-Mart Stores Inc. as a major retail customer.

Dean, which estimates it buys about 10% of the raw milk produced in the U.S., forecast earlier this year that the cost of the commodity would rise 17% in the first quarter compared with the end of 2013. Surging exports of U.S. dairy products to China and other Asian countries are driving up the cost of key dairy components such as milk powder for processors like Dean.

"Fiscal year 2013 was challenging for Dean Foods," company officials wrote in Friday's filing. As a result, senior executives received no short-term incentive pay tied to the company's performance last year, according to the document.

Dean reported a $37.7 million fourth-quarter loss in February.

Shares in Dean were down 1.1% Friday at $15.18. The stock has fallen 11% so far this year.

Write to Jacob Bunge at jacob.bunge@wsj.com

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